okay, I checked the doubling on an XP30 using Cakewalk 8. Absolutely NO info on channel 16. So perhaps the problem is corrected in the xp30. However, the first thing, as Dnarkosis said, this problem reminded me of was the controller channel parameter. I have noticed the parameter being switched back to it's original value (16) automatically. Very strange.... so maybe these problems are interrelated.
maybe it's a sequencer problem. Perhaps your sequencer is independantly doubling the info because both sequencer and JV/XP unit are trying to direct the info to a channel.

furthermore I experience very frequent timing problems especially when two or more program changes are sent on different channels and when there are lots of controller data events like pitch bends sent.