Try running only Atari's official patch 2 and then a fan fix called temple.zip instead of patch 3. It's unofficial, but better-behaved, and is compatible with further modding, which 3 is not. If you still have this failure to boot problem, there is a workaround we can discuss. But try temple.zip first.
Get it here.
Temple.zip
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http://www.jadri.com/temple.zip
-or-
http://www.co8.org/files/patch/temple.zip
1. Unzip the patch. (Double click the folder you downloaded and choose the extract all files option in the corner of the window (XP))
2. Find the file in you GAME'S directory called "temple.dll" and remove it. (Put it somewhere you can find it again.)
3. Take the "temple.dll" file from the unzipped patch folder and put it where the original file was.
4. Inside the patch folder should be a folder called "data". Inside that folder should be three new folders. Take all of them and put them into the game's "data" folder.