Cryptnite-qt is trying to download blockchain into %appdata%/Bitcoin and corrupts Bitcoin blockchain (Windows 7 x64). The wallet seems to have same path that Bitcoin-qt has (probably something wrong in the Windows registry).
It's actually Bitcoin trying to read the Cryptonite data folder, but the issue has been fixed. You might still be experiencing problems because you ran an older version of Cryptonite and your registry is still messed up. To repair bitcoin, open regedit and search for bitcoin-qt. Should be a key called strDataDir in there, point that back at your bitcoin folder and everything should be fine. If that doesn't work or you can't figure it out, reinstalling bitcoin should also fix your registry.
Thanks. Dowloading the newest build fixed the problem but now I'm stuck on downloading headers. There are lots of lines in debug.log like these:
2014-08-16 08:33:58 ProcessBlock: ORPHAN BLOCK, prev=0000000001a33261995f32364c0d1fc3ebbd011faa2237de75e9dfd31721fef2
2014-08-16 08:34:00 ERROR: AcceptToMemoryPool: : transaction not final
2014-08-16 08:34:03 ERROR: AcceptToMemoryPool: : transaction not final
2014-08-16 08:34:05 ERROR: AcceptToMemoryPool: : transaction not final
2014-08-16 08:34:07 ERROR: AcceptToMemoryPool: : transaction not final
2014-08-16 08:34:26 ERROR: AcceptToMemoryPool: : transaction not final
2014-08-16 08:34:44 ProcessBlock: ORPHAN BLOCK, prev=0000000000de609c3d17817a61cd822e3366f159dc5180e3f03aeb6534de5edd
2014-08-16 08:34:44 ProcessBlock: Orphan already exists! 00000000018bff0056cd2efbd99cb6ff581f12ee286c1bc828e37c4c3fe7cf81
2014-08-16 08:34:46 ProcessBlock: ORPHAN BLOCK, prev=000000000135a7bc1ff07224e6672afac943f56497219a022d130ecd1a0f258a
2014-08-16 08:34:46 ProcessBlock: Orphan already exists! 0000000000de609c3d17817a61cd822e3366f159dc5180e3f03aeb6534de5edd
2014-08-16 08:34:53 ERROR: AcceptToMemoryPool: : transaction not final
2014-08-16 08:35:03 ERROR: AcceptToMemoryPool: : transaction not final
2014-08-16 08:35:08 ProcessBlock: ORPHAN BLOCK, prev=00000000018bff0056cd2efbd99cb6ff581f12ee286c1bc828e37c4c3fe7cf81
2014-08-16 08:35:08 ProcessBlock: Orphan already exists! 0000000001a33261995f32364c0d1fc3ebbd011faa2237de75e9dfd31721fef2
2014-08-16 08:35:24 ERROR: AcceptToMemoryPool: : transaction not final
2014-08-16 08:35:28 ProcessBlock: ORPHAN BLOCK, prev=0000000000e9ee8189ef0ad8c27c8ff488fbed12dcbf929053caab45e7438022
