On my primary Indexer (~10GB / Day) I got the following errors, almost exactly every minute:
10-05-2011 07:21:49.539 -0400 ERROR FSChangeMonitor - Exception thrown in update(2) - continuing
10-05-2011 07:21:49.539 -0400 ERROR SQLitePersistentStorageImpl - Error executing: select primarykey, value from keyvaluepairs_t where secondary1 = ?1 Msg=database is locked
Restarted multiple time, I believe I got only 1 instance running (2 processes)
It looks like there is a lock on the database. Did you try to restart your splunk instance? Is it possible that you've got another sql lite tool accessing these files?