Re: Receiving many more rows than expected

The problem is that sometimes (once every few days at about 2-300K queries per 
day) I get many more rows than the max 5000 I asked for (I've seen up to 25k). 
And I'm getting timeouts and other problems as a result.

I would bet you have another copy of the code running without the limit. Maybe on a cron job.
To prove this, modify the log statement slightly and see if this statement is really returning more then 5000 rows.

LOG.debug("1 - Fetched %d rows", rlen) or similar.