I don't remember what I did yesterday, but I found the bug:
The old rainbow tables assume a charset of size 16. You can see this in
rainbow chain length verify fail
      index to verify 73353250
 actual index 5006754073353250
 so that doesn't match. This is kinda bad news, because it means I have
 to port over rtgen, but it's good news because the tables are probably
 going to get much smaller.

 Changes are probably debug related, everything is solid enough up to
 here. CUDA doesn't work yet (no GPU in my computer, files don't get
 compiled in).
added RainbowTableGenerate and modified makefile to compile pangen.
fixed typo in makefile.
Ported RainbowTableGenerate over to rcracki_mt version.
Surprisingly easy.