All my pets appear to have stopped regenerating energy shortly after the new day started.

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I'm appearntly not the only one with this problem and the islands aren't regenerating either.

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(Hopefully the last edit) A little more investigation and pregnancies, quests, and training seem to be proceding normally this time unlike the last time I reported a problem like this. http://beastkeeper.com/thread/4656

This seems to be happening to me as well, but not to all my pets.

There really was a problem that stopped all timers this night. It was fixed this morning. Sorry for the inconvenience.