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I can't tell how many locations you found the file: java.exe in. It looks like there could be more than one but I don't understand what you have posted.

Does Win8 change what you ask to find in...

There may be more than one.
Do a search for java.exe on the C: drive to see how many versions there are. I have one at:
C:\Windows\System32\java.exe

Also look at the PATH to see which folder is...

What was different between using the commandline from the registry (this one failed)
and manually entering the commandline (this one worked)?

Was the java.exe file that was used with the manually...

If it works in the command prompt then the commandline used by the OS must be causing the problem.

Slow that down by openning a command prompt window, changing to the folder with the jar file and entering the java -jar command.

Here's an export of the jar file enty:

When you click on a jar file, the OS needs to find a commandline to use to execute the code.
When you type in the commandline to execute the jar file, it skips having the OS build the commandline.
...

If the jar file's contents executes OK with a manually issued java command, then the problem could be with the OS when it tries to execute the jar.

Try running the jar file in a command prompt window to see if there are any errors.
Open a window, change to the directory with the jar file and enter the command:
java -jar AnotherGrep.jar...