Finally got a response by emailing EHX directly:

“If a loop is playing and you want to change loops using the 45000 Foot Controller, it does so after the current loop plays out to its end. So you queue up the next loop, it does not change immediately.

Let’s say you have Loop 2 playing, with 3 bars left on the loop. Then you press the UP FSW twice for Loop 4, the number 4 is blinking on the 45000’s Foot Controller display. When the Loop 2 comes to its end, Loop 4 will begin playing.”

It would be nice if an EHX employee could monitor these forums and answer simple questions like this one, especially for those who have recently plopped down $500 for one of their products and is ready to plop down more.

Nevermind, figured it out!

They need to be mono! (except for the stereo mix down track)

I guess I should have realized that, but a reminder in the manual would’ve helped