I'm pretty sure I ran into a similar issue the other day. It was weird, it had been working normal earlier and then all the sudden, during the same session, it didn't. Only one layer's polyphonic sequencer would play, and if I switched layers and hit play on the other layer, then the first layer would stop and vice versa.
I was eventually able to solve the puzzle - it was user confusion - but I can't remember off the top of my head what I did to get it back to normal. I can double check later when I'm at the synth and figure it out again what I had done. But in the meantime, here's a clue for your investigation. I had gotten the synth in this state somehow by switching between layered and monotimbral modes and also switching between the poly and gated sequencers. Changing it back involved undoing whatever I had done when switching between the layered modes. I had a bunch of weird stuff going on with the rev2 that day, this issue was just one among other confusing and surprising finds, which is why I can't remember exactly what I had done.
For example, during this session I discovered that you actually *can* use the poly sequencer at the same time as the gated sequencers as long as it's being clocked with an external trigger/gate via the sequencer jack, which is how I usually jam. While the poly sequencer play button is lit, hit the sequencer mode button. Now it's in gated sequencer mode and you can edit them as usual, but the poly sequencer is still active.The poly sequence is stepped through with triggers, and the gated sequencers follow the midi bpm or midi key presses depending on your settings. I'm not sure if I'm, like, breaking the law, but it doesn't seem like something that would harm the synth by using it like this. That's just my uneducated guess though.
Another related finding from the same session - even in monotimbral mode, you can get the rev2 to play the poly sequencers of both layers - so the sequencers of both the active and inactive layers play the active layer's voice. In usual situations, you probably don't want that, though I can see potential uses. Anyways, somehow while playing with the first discovery, I got it into this mode and I think while I was trying to get it out of this mode that I somehow got the rev2 into the state where only one or the other poly sequencer would play.
I hope that all made sense and that it's helpful. Like I said, I can see if I can reproduce the situation later and figure out what I had done to get out of it.