Well the only problem with the pthread.h and other related compilation problems is that somebody (for some unknown reason) decided to change the OS defs from _WIN32 to _WINDOWS which breaks windows compilation as there's no such definition according to MS. There's about 170 or so of them that I've replaced in my copy of the source from what I remember in my find and replace.
For those that wish to know more, pthread.h and a couple others are *nix specific headers relating mostly to threading, since *nix is typically posix compatible and windows is not.
To break it down even further, since those of us with this particular problem are on windows platforms it's looking for _WINDOWS to be defined, and since it isn't VS skips to the else section which is for *nix. In other words not a IDE problem, but a problem resulting from attempting to program for multiple platforms without knowing the proper OS defines.
Now to figure out why my eqlaunch is complaining about unresolved zlib externals when it shouldn't be...