Lets throw insuring you haven't reached/exceeded your quota to the mix too. I use ubuntu but not mysql and have no issues at all. Let's also try disabling mysql and see if you can save to flatfile.
The server i got access to have ~140GB free, and hasn't quota enabled on users.
The server i don't have access to atm have something similar free, and doesn't either have quota enabled.
Services runs under the same account as the ircd, and both servers are low usage (so the file descriptor limit isn't reached).
The problem is there, doesn't matter if i run it with mysql or flatfile, it still happens from time to time.
And as i mentioned in my last post, a quick tail on the backup *.db files showed that one or two of 'em seemed to have been cutoff somewhere in the middle (they didn't get down to the OS STATS at the bottom that i observed in all the others *.db) and lacked a \n on the row it got cutoff also.