Unfortunately there are too many possible reasons to have an educated guess without further information. Could you please to some command-line debugging as described here: http://fiji.sc/wiki/index.php/Debugging#Command_line_debugging ?

Thanks.

I´ve done the command line debuggin and here is the error:
Microsoft Windows [Version 5.2.3790]
(C) Copyright 1985-2003 Microsoft Corp.

C:\Documents and Settings\sidnei>cd..

C:\Documents and Settings>cd,,
C:\Documents and Settings

C:\Documents and Settings>cd..

C:\>cd Program Files

C:\Program Files>cd FIJI
The system cannot find the path specified.

C:\Program Files>ls
'ls' is not recognized as an internal or external command,
operable program or batch file.

C:\Program Files>dir
 Volume in drive C has no label.
 Volume Serial Number is 846F-1203

 Directory of C:\Program Files

29/02/2012  10:56    <DIR>          .
29/02/2012  10:56    <DIR>          ..
25/03/2010  11:10    <DIR>          Alwil Software
29/02/2012  10:56    <DIR>          Common Files
09/06/2009  14:41    <DIR>          ComPlus Applications
14/10/2009  16:08    <DIR>          EPSON
15/03/2012  14:49    <DIR>          Fiji.app
24/10/2011  19:57    <DIR>          Gatan
16/02/2012  02:01    <DIR>          Internet Explorer
09/02/2010  15:33    <DIR>          Java
27/10/2009  16:12    <DIR>          Logitech
29/02/2012  10:57    <DIR>          Materialise
09/06/2009  17:47    <DIR>          Messenger
09/06/2009  16:50    <DIR>          Microsoft IntelliPoint
09/06/2009  16:49    <DIR>          Microsoft IntelliType Pro
10/06/2009  11:05    <DIR>          Microsoft Office
14/10/2009  17:30    <DIR>          Microsoft Sync Framework
09/06/2009  16:18    <DIR>          MSBuild
09/06/2009  17:48    <DIR>          MSXML 6.0
09/06/2009  14:40    <DIR>          Online Services
16/12/2010  02:04    <DIR>          Outlook Express
16/02/2011  15:04    <DIR>          RealVNC
09/06/2009  16:14    <DIR>          Reference Assemblies
14/10/2009  17:30    <DIR>          SyncToy 2.0
10/06/2009  12:44    <DIR>          totalcmd
27/10/2011  16:10    <DIR>          Volume Graphics
10/06/2009  13:25    <DIR>          Windows Desktop Search
09/06/2009  14:40    <DIR>          Windows NT
18/05/2010  18:03    <DIR>          WinRAR
               0 File(s)              0 bytes
              29 Dir(s)  14.922.813.440 bytes free

C:\Program Files>cd FIji.app

C:\Program Files\Fiji.app>fiji-win64 --console

C:\Program Files\Fiji.app>Exception in thread "main" java.lang.NoClassDefFoundEr
ror: imagej/ClassLauncher
Caused by: java.lang.ClassNotFoundException: imagej.ClassLauncher
        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
Could not find imagej/ClassLauncher

What should I do? Reinstalling FIJI from a fresh download will correct it?

Still missing some information. Could you also use the option "--dry-run" to show the command line Fiji would use with the system Java?

P.S.: when pasting the output of the command line, showing wrong attempts such as "ls" or "cd,," or "cd FIJI" is not necessary... ;-)

Here it is
C:\Program Files\Fiji.app>fiji-win64 --console --dry-run

C:\Program Files\Fiji.app>javaw -Dpython.cachedir.skip=true -Dplugins.dir=C:\\PR
OGRA~1\\Fiji.app -Xmx6135m -Xincgc -XX:PermSize=128m -Dsun.java.command=Fiji -Dj
ava.class.path=C:\\PROGRA~1\\Fiji.app/jars/ij-launcher.jar -Dimagej.dir=C:\\PROG
RA~1\\Fiji.app -Dij.dir=C:\\PROGRA~1\\Fiji.app -Dfiji.dir=C:\\PROGRA~1\\Fiji.app
 -Dfiji.defaultLibPath=bin/server/jvm.dll -Dfiji.executable=C:\\Program\ Files\\
Fiji.app\\fiji-win64.exe -Dij.executable=C:\\Program\ Files\\Fiji.app\\fiji-win6
4.exe -Djava.library.path=C:\\PROGRA~1\\Fiji.app/lib/win64 -Dsun.java2d.noddraw=
true imagej.ClassLauncher -ijclasspath jars/ij.jar fiji.Main -port7
^A

Do you have C:\Program Files\Fiji.app\jars\ij-launcher.jar? If yes, does it contain the file imagej/ClassLauncher.class ? (A .jar file is really a .zip file; you can rename it and double-click on it in the Windows Explorer; just remember to rename it back before you try again to run Fiji)

Hi Johannes, I REALLY appreciate your timely support. 

NO, I don´t have the ij-launcher.jar in the jars folder.

Is it possible that the ij-launcher.jar file is stuck in C:\Program Files\Fiji.app\update\jars\ij-launcher.jar?

If not, I have no idea at what stage it left (or maybe the Updater never realized that ij-launcher.jar is a dependency of the launcher?)...

So if that happens, if there is no ij-launcher.jar to be found anywhere in C:\Program Files\Fiji.app or any of its subdirectories, the only solution I have to offer is to download http://jenkins.imagej.net/view/ImageJ/job/Fiji-minimal-daily/ws/fiji/jars/ij-launcher.jar and put it into C:\Program Files\Fiji.app\jars\ manually. After that, Fiji should start (and you might want to run the Updater first thing, to fix whatever else is missing).

This is getting really confusing. Responding to your first question:
Is it possible that the ij-launcher.jar file is stuck in C:\Program
Files\Fiji.app\update\jars\ij-launcher.jar?

THERE IS NO SUCH FOLDER IN MY INSTALLATION. I only have the following subfolders: images, jars, java, luts, macros, misc, plugins, retro, scripts.

I did download the ij-launcher as you suggested and put in the jars folder, but FIJI still has the same weird behavior: the icon flashes but it does not start. 

Now I would like to know if just reinstalling it from scratch would fix it or that would not work?

Thank you again.

Could you please do the --console --dry-run thing again?

Here it is:
C:\Program Files\Fiji.app>fiji-win64 --console --dry-run

C:\Program Files\Fiji.app>javaw -Dpython.cachedir.skip=true -Dplugins.dir=C:\\PR
OGRA~1\\Fiji.app -Xmx6135m -Xincgc -XX:PermSize=128m -Dsun.java.command=Fiji -Dj
ava.class.path=C:\\PROGRA~1\\Fiji.app/jars/ij-launcher.jar -Dimagej.dir=C:\\PROG
RA~1\\Fiji.app -Dij.dir=C:\\PROGRA~1\\Fiji.app -Dfiji.dir=C:\\PROGRA~1\\Fiji.app
 -Dfiji.defaultLibPath=bin/server/jvm.dll -Dfiji.executable=C:\\Program\ Files\\
Fiji.app\\fiji-win64.exe -Dij.executable=C:\\Program\ Files\\Fiji.app\\fiji-win6
4.exe -Djava.library.path=C:\\PROGRA~1\\Fiji.app/lib/win64 -Dsun.java2d.noddraw=
true imagej.ClassLauncher -ijclasspath jars/ij.jar fiji.Main -port7

And without --dry-run?

Here it is, but I had done this before ...
C:\Program Files\Fiji.app>fiji-win64 --console

C:\Program Files\Fiji.app>java.lang.ClassNotFoundException: fiji.IJ1Patcher
        at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
        at java.security.AccessController.doPrivileged(Native Method)
        at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
        at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
        at imagej.ClassLauncher.patchIJ1(ClassLauncher.java:99)
        at imagej.ClassLauncher.run(ClassLauncher.java:71)
        at imagej.ClassLauncher.main(ClassLauncher.java:22)
Class 'fiji.Main' was not found

You might have noticed that the error message is now different? Instead of imagej.ClassLauncher it cannot find fiji.Main. Meaning that not only ij-launcher.jar is missing, but also fiji-compat.jar. And most likely that's not the end of it, I would wager a pint of beer that ij.jar is also missing.

So something really did not work well with that update, and I guess it has to do with the idea Windows has of security, not letting programs update themselves in-place without administrator's privileges when they are installed into C:\Program Files.

However, that is exactly what seems to be the case in your setup.

My suggestion, as always, unpack fiji-win64-<date>.zip to your desktop and start it from there.

OK, I think your guess regarding Windows behavior makes a lot of sense.
I did unzip the application inside a desktop folder and it runs fine. Except
that the attempt to update the updater fails, as it used to do in the past.
However, it does create the Update folder this time. 

I then simply quit FIJI and started it again and it is doing a major update.
Let´s see how it goes. I will also reinstall my previous plugins.

I think that settles the issue, right? I will not close the bug report in case
you want to add some more info, but I am satisfied on my side.

Thank you again,

Well, it is really only a work-around, but time pressure does not allow me to look int this issue more closely for now. Anyway, it seems you're back in business!