It isn't super important to do (it is like a db defrag), but that yours fails is not generally good news. Your client working otherwise suggests this is an unusual permissions issue rather than an actual problem though. Maybe an old instance of the client executable hanging around somehow?
This message suggests it is failing as soon as it opens the file, right when it starts–is this true, or do you get this error ten minutes into the operation?
If you shut down your client and go to install_dir/db and then run the sqlite3 executable and type this:
.open client.db
VACUUM;
.exit
How does that work out? Do you get a better error? You might like to try it for all four of the .db files there, although be warned that the mappings one will take a while to finish.
Unless we figure this out quick, you probably want to turn off the auto-vacuums for now under options->maintenance and processing.