I downloaded a newer version of Matlab (2011a) and installed Java on the clean machine before running ThinApp and it still gets the errors up above. If I go past the error and go to the drive share that holds the exe of the program, I am able to double click on it and run it without any errors. Does that help? I gave Domain Users rights to the folder to see if it was a rights issue and it does not seem to be.
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