When I first installed JRiver, and used JRemote it would seem to work fine, then the screen would "reboot" back to the empty JRemote screen, and then I could sometimes browse the music, and sometimes it would hang/pause. Other times it wouldn't be able to connect to JRiver at all. I would then restart JRiver, and it would work for a little bit and then it would start happening again.
I had my system pointing to a specific folder to auto import when new content was copied over. I turned off auto import, and just manually import new folders now. JRemote has had no issues for me since. I will look through my settings later and see if maybe I turned something else off while I was tinkering.
I have not experienced any of your glitches that you listed other than the pauses. (Which I fixed) I use a retina ipad for JRemote.
How about using Webgizmo? Does the same thing happen using that? I think JRemote is just a front end to Webgizmo. You can try it here:
http://jriver.com/webgizmo.html