Although it looks as though you're doing a lot more with your MPC than I did (I have a MPC 1000), I didn't have any problems such as those you describe. However, it did take a while to get all the MIDI setting correct so that everything worked (almost) smoothly.
I say almost smoothly, because as I set things up on the Rev2 Global menu, I often found that parameters were affected that I wasn't expecting, and, as your going backwards and forwards on the keyboard and Global parameters you often forget something, or not realise that it should be set differently.
As an example, make sure that your midi channels are set correctly between layer A and B. I often forgot, and ended up wondering why a sequence was being triggered. Or, that the correct (for you) clock was selected. It also took me quite a few tries to get the banks to change to where I wanted with both the MPC and Reaper also.
Anyhow, one thing that would be really useful on the Rev2, would be a 'midi set' button, which once you have the parameters set, you press 'midi set' and it saves those settings. If you wish to return to your keyboard and not use midi anymore, you just de-select 'midi set'. This would save going backwards and forwards in the Global settings, which often leads to parameters being changed, which you then forget later when going back to midi (or the other way around).
Sorry if I can't be anymore helpful than that, I hope you find a solution. If not contact the DS team (via email), they're always very helpful and may well have a solution or explanation for you.