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Does running things in "compatibility mode" actually make any difference? Personally, I don't think it changes anything. For example, i was running NBA Live 2k1 on my Windows98se system and after moving to winXP the game doesnt work. I tried running it in any number of compaibility settings and it still doesn't work. The same proved true for Maya and 3dsmax.

It depends on the applications
For maya and 3dsmax. You should upgrade version of cdilla (the manager for the license)
for games, it does a change but not for all games. IT made a change for old dos games and applications on my side. But most current games, it doesn't change anything