Nokon, don´t work liner brakes. Haven´t got our Jagwire sponsored cables yet. Love the bike for it´s ride and weight, but all 28 team bikes has the problem.
Got some pics? As @Winguy asked, are you using the supplied derailleur housing cable for the rear derailleur (comes in the box with the rear derailleur and is different that the piece supplied in the standard cable set). It is unique and different, with the steel wound inside like a brake cable housing versus a typical derailleur housing.
Also, having installed a few 9100 systems lately, removing a rear wheel can be problematic with the new 9100 derailleur. You need a lot more space between the bottom bracket and the tire to be able to move the wheel forward a good amount for easy removal. Despite some rumors that the new derailleur, with it's little extension thingy in lieu of a direct mount hanger, makes for easier wheel removal, this is simply not the case with a lot of existing road bikes it seems. It does allow the use of a larger cassette, but once again... road bikes are not mountain bikes. Shorter chainstays and/or lots of material around the rear of the BB can make for much more difficult wheel removals than with the 9000 series stuff. One frame that had I had no issues with is the Trek Emonda, due to it's great clearance all round the entire wheel, including the bottom bracket area. Another frame, but same setup, was not so lucky and proved to be a real pain in the ass for wheel removal due to the large amount of material behind the bottom bracket. Maybe in your case it's a combination of the new 9100 stuff in conjunction with the Cannondale frame. I haven't checked out the Cannondale frames in any detail with respect to how the new 9100 stuff works with it, but sounds like it may not be so great.