I'm not sure what is going on but all my sqlite3 databases are locked. I have tried everything suggested for unlocking them but nothing works. I have no shells open or any running processes that could hold connections open to those databases. Fortunately they are not that important and can be recovered after about a days worth of work but I would like to know why exactly this happened. I'll leave those database files around so somebody can take a look at them.
I have downloaded one of the locked files to my windows box and I can open it and browse around with SQLite Manager add-on for firefox. Let me know if there is any other information I can provide for troubleshooting the issue.