I started having just this problem over the weekend while riding around the Paonia Colorado area. It's around 5000 ft elevation but I'm not sure that had anything to do with it.
It would run rough at between 4K - 5K then suddenly kick in and just leap. A few times I was standing up briefly to stretch the legs and hit that spot and it jerked my arms so hard I nearly fell off backward.
Every time I would stop for gas or for lunch or for a break, the bike would either run great like it's supposed to with the FCE or it would run crappy like I had water in the gas or was missing a cylinder or two. If I stopped and turned off the engine, next startup was a crap shoot as far as how it ran. It was like this for 3 days over the weekend trip.
I haven't had time yet, but I think I may have a loose connection in the wiring so I'm going to take everything apart this weekend and have a look at it again. When I installed it, I crimped and soldered the connectors to the wiring but am relying on the connector to connector junction for the integrity of how it is hooked into the system. I will also put some dielectric grease on the connections. If I am still having this intermittent behavior I will remove it and then see how it runs.
I'm hoping it's just a connector problem. The bike has 18K on it now and it may be due for plugs, etc. but when I purchased it from the PO last year, he had just had it tuned up at 7K so I'm not thinking it's a plug problem. Anyone else have any suggestions of what to look at?
When it's running like it's supposed to with the FCE, it's wonderfully smooth!

But when it's not, it's way worse than it was stock with just that annoying little cutoff in the 3500-4000K region.