We just started experiencing the problem with records entered over the weekend, so we must have crossed a threshold. It seems to definitely be a query that's taking too long. I've only got about 300 records in the event I'm trying to pull a CSV for, so it's not even that much data. I can work around the problem by changing which fields I select for the export. I don't know if that will work for others with more records.
Updated to DTRegister 2.7.2e this morning, but it doesn't seem to have helped.