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Yup, if the software expects to be running as console/GUI - and what software wouldn't?! - then changing its subsystem will make it go completely crazy. I just tried it with one of my own programs, originally console and hacked into GUI: after processing its input and sending the results into its output (redirected into a file so that I can see it really did something), it keeps running as if it is unable to realize that its input has ended.
(For hacking executables, Hacker's View is probably your best choice.)
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Joe Forster/STA
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