Saved .bitcoin directory full ~9 GB block data, won't work when copied to another system
Two things come to mind as possible reasons.

The most probable reason is that you've switched client versions. There was a switch between 0.7 and 0.8 in how the block index (not the block data itself) was stored; it was changed from BerkeleyDB to LevelDB. If you remove the blkindex.dat (and really want to keep an index around, which is unlikely) you can restart the client with -rescan and -txindex. It will take a while (an hour?) to complete the indexing.

The other reason that I can think of is that it's genuinely corrupt, but that's unlikely.