Ok, so I found my problem so I retract my question. Apparently the problem came from bad data. Well, to me it's bad data, but whatever. I had set a couple of properties on my table to be fetched eagerly. This of course results in a join. The problem was that some of these records had nulls for the properties I was trying to join on. This caused the join to not work and the record was not returned so I was getting fewer records than I should. I fixed this by complaining about the bad data, fixing these records to not be null for these columns. The other fix, of course, could be to use an outer join.
Weird symptoms. Anyway, it's fixed now.. :)
--Krullshards
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