It was my first time using the me system in the last few days and landed on a weird outcome that might be similar to yours. I had patched keys, keys2, gtr, acoustic gtr, vox1-5 to ME channels 5-13 respectively on an SQ, however on the ME-500s they showed up as channels 1-9. It’s my assumption now that on the 500s whatever you assign first goes to the first available channel rather than what is specified.
So with that experience in mind, is what you patched in order, but not in the right ‘slot’?