When I run with -checkblocks=0 -checklevel=2 on master, I get the following error:
2014-05-29 06:53:38 ERROR: CheckBlockHeader() : block with timestamp before last checkpoint
2014-05-29 06:53:38 ERROR: VerifyDB() : *** found bad block at 278999, hash=0000000000000001ed51db67f98e83ac76209fe00dabc2a42c80cbc9a4ef6c45
We've discussed on IRC a bit and @gmaxwell was able to reproduce it, so it's not local corruption. Seemingly it picks 279000 as last checkpoint instead of 250000 for block 278999.
This problem does not exist on the 0.9.2 branch, so it must have been introduced in one of the recent changes in main.cpp/h.