Maybe you are on the wrong starting directory. Should that be bitmonero-master/build?
Good call. I guess I assumed the source directory was the actual src directory and not the root of the github pull. This allowed me to build but when I run the bitmonerod.exe file built, it crashes with the log pointing to:
2015-Apr-09 06:01:49.582503 ERROR C:/msys64/home/user/bitmonero-master/src/daemon/daemon.cpp:145 Uncaught exception! Failed to initialize core
2015-Apr-09 06:01:49.582503 Deinitializing rpc server...
2015-Apr-09 06:01:49.582503 Deinitializing p2p..
I don't recommend compiling from git head if you want it to be stable, we've *just* done a bunch of merges and there are known issues as well as other unexpected hiccups. You can checkout the 0.8.8.6 git tag if you want a more stable build.