I solved the problem. The issue was that theano.config.floatX was float32 and not float64, which I think makes pymc3 use int16 instead of int32. Thus Y in the code you linked would be int16 (while the test values were of type int64). Simply changing theano.config.floatX to float64 solved this problem.
Thanks! I would never have figured out this was the issue without your help.