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Showing developer posts only. Show all posts in this thread.
When you say the EXE changes, is that just the result of applying the patch?
And the "original EXE you replace it with is that the One from the CD or the one from 1.3A patch?
 
The EXE should never be altered, except by applying a patch.
Theirfore I would check your system for Viruses.

Also What publisher version is this? the publishers logo should be on the CD beside the Paradox logo.