I'm not following.

A. What is the unwanted silence from? Did you import the BB tracks at the very beginning of the Reaper project?
B. Your keyboard should play the desired loop when you hit a key (somehow). Just start recording and hit the key when you want it to start playing. How are you triggering the loop from the PA900? Is the PA900 what is giving the delay before starting?

One option is to let it record out of time (but at the same tempo) and then drag the keyboard to line up with the rest of the project .. but that's a pretty clunky way to go.

I do not work here, but the benefits are still awesome
Make your sound your own!