I'm sure the real pros will come in with the more exact answers, but I can tell you hops definitely do not stop bittering at flame out. As you suspect they continue to release bitterness as the wort cools. The lower the temp gets the slower they bitter.
If one of your 5 Gallon batches remained hot longer than the other, yes it stands to reason it would have more IBU's than the other, assuming the hops remain in the wort as it cools.
To help combat this you might try adding your hops as whole leaf in a sock, and removing the socks at the same time from the entire batch. This should keep the hop signature fairly similiar in both halfs of the batch.
Still a good idea to get that second batch under 100 as soon as you can though.
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