I appreciate the efforts here. I tried make depend, but it hasn't made a difference unfortunately. I'm using the latest version of TortoiseSVN and mingw-mame-w64-20110519.exe (found here: http://mamedev.org/tools/) on Windows 7 Home Premium 64-Bit.
Do I need to update mingw64? I had attempted to do this from here (http://sourceforge.net/projects/mingw-w64/files/mingw-w64/mingw-w64-release/) although I think I downloaded the v1.0.4 instead of v2.0.4, but inside v1.0.4 there was no bin folder with make.exe etc... So I'm not sure what to download other than what is on the mamedev website. I guess I can try and download the revision before the MegaCD changes were made and see if I can compile the source, but I'm not sure what to do if releases after that won't compile.