Which VC and which gcc?
For example (and these are off the top of my head as issues that have affected me) VC6 has the for-scope problem, VC7 must have inner template classes defined inline, numeric_limits didn't appear until gcc3 ...
And how much of the windows api? Lots of windows and COM objects or are you just using structures like BITMAP?
Maybe you should consider running the application through wine
http://www.winehq.com/ or more specifically using winelib, seeing as you skipped the MFC (I don't blame you) -
http://www.winehq.org/site/docs/winelib-user/index ?
I think that you can find a portable thread library at
http://www.boost.org - I haven't used this library myself but their other stuff has been pretty useful.