You are correct, there are differences between the versions, but these are not subtle hidden issues/bugs. They are well documented changes/differences. There is a huge difference between the two.
Not everything is that obvious. The inability to install government made patch for HKSCS in Win2003 Server is not known to us until we try to install that and the server won't boot even to safe mode afterwards. We do it again on clean installation and fail again to confirm this. And you'd think since WinXP and Win2003 use the same kernel, software that can run on WinXP could be pretty sure be able to run on Win2003?
Because the HKSCS character "邨" (which means "estate") appear in 20-30% of Hong Kong addresses, inability to handle this on the server is a very significant bug to us. Actually we even created a test case specifically testing for this - just that the tests are only run on WinXP and never on the server before UAT.
After this incident, it's very clear to me that if you're going to support a platform, you have to debug the program on the platform the software is going to run on.