Ok, I found a way to reproduce this bug.
When Podium records notes on a blank track, it creates a sequence event and snaps the sequence event start to the previous bar line. But it creates the sequence when receiving the first note off message, so that it knows how long the sequence needs to be to hold the note. If you press and hold the first key, and let the play cursor move across the next bar, and then press and release a second note, then the sequence will be created based on the second note, and not the first note that is currently being held. When the first note finally is released, it will have a start time earlier than the sequence event, and thus will be discarded. I’ll change this, so that the created sequence considers the start time of any notes currently being held. Sorry for the long explanation.
However I could not make the first note skip recording if I enabled punch in and set the punch in position prior to the point where I press the first note. Could you check if you manage to record the first note when using punch in?
Oh, and thanks for your help with hunting down this bug.