Doesn't this sound like a corrupt database? Did your machine crash at any point when playing with bitcoind and bitcoin?
No, there is no crash. BTW
bitcoin and
bitcoind from sourceforge are mutually compatible. But bitcoind from Debian repositories gives the reported problem with both.
I've found a trick to share de same directory. It's not fair play but it works.
After stopping either
bitcoin or
bitcoind (from SF), delete the file
~.bitcoin/database/log.0000000??, and also eventually
~.bitcoin/bitcoin.pid. Then launching
bitcoind from Debian packet yield no problem. Before re-run the programs of SF, the same file deletion should be done.
I'm not sure why, but it solves the problem...