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I have the same problem, first I bought, after I read the forum.
Namur: I solved that freeze at my end (on Win7 64) by changig the compaytibility settings on the shortcut from Win98 to Win XPSP2. At least one more user reported this also worked for him. Have you tried it ?
This along with the new executable posted by support helped me get past the second guards! I hope it doesn't freeze again... I'll report if it does. Thanks!

Update: It froze again a couple minutes past that point, but since I've switched to WinXP SP3 in the compatibility tab and disabled "Threaded Optimization" in the NVidia control panel for the game's executable (Atlantis.exe) I haven't had the problem so far.
Post edited March 01, 2014 by MrAlphaNumeric
I have CD original version and crash on windows 10. I don't know if gog version own the last version of this game but I have install the last patch (patch 3.0) of this game and no crash