python-2.5.2-r6 has been emerged with USE=-sqlite, sqlite-3.5.9 is installed though. the python package contains /usr/lib/python2.5/lib-dynload/_sqlite3.so which should not be the case.
Seems solved for me with 2.5.4-r3
This bug seems to be fixed in dev-lang/python-2.6.2-r1. I also fixed it in dev-lang/python-3.1.1.