Sorry to let you in on this one mate, but I had a JV2080 for a year and a half, and it took me a while to work out it was the 2080 that was causing midi timing problems. Their crap timing is caused by roland using the same processor as the 1080, but making it produce 3 efx's rather than 1, in other words the processor aint fast enough to handle the amount of data. I tried everything with Roland, they took the unit back etc, but got stuff all out of them.
My advice to you is to watch tight envelope settings, lots of lfos and big layered sounds all screw timing up. Oh and dont use too many voices, anything over about 20-30 i found timing got progressively worse. (Seems abit mad forking out for a 64 voice synth doesnt it?!)
Unfortunatly, there is nothing else you can do, I sold mine as i was so cheesed off with it, Ive got a 5080 now, it's too early to say whether this thing has got similar problems, as im not using anywhere near 128 voices, but from what ive heard Roland are now using seperate processors for the effects which means that the synth engine has the same power as the xv3080