If it helps anybody, last weekend I was finally able to build the client on x64 windows (using windmaster and floodyberry's github projects). I'm not sure why people say scrypt won't compile on windows, I don't recall having issues with that part.
If you were working from floodberry's github repository, that's a newer version of the scrypt-jane library that reportedly has been corrected to compile cleanly. Previous version did not, due to the SSE instructions.
If nothing else it gets rid of the checkpoint message.
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I didn't post it right away because nobody knows me and I didn't want to be accused of adding malware. Maybe someone trusted in the community could check it out. If you have any doubts, don't download it please.
Hanzac already released a 64-bit Windows build based on my GitHub repository about 2 weeks ago after I fixed the checkpoint warning. Multiple people have checked it out and haven't observed it to do anything suspicious or unusual:
https://bitcointalk.org/index.php?topic=206577.msg2207446#msg2207446