Agent K

As your problem seems to be much worse than mine you could still try without mods. So I guess you are talking about something else than that slow and steady descent on orbits that should be considered stable. Rocket made of 9 parts, 1.1.2 x64, orbiting Kerbin, Ap 630 km, Pe 118 km. Result after orbiting from Pe to Pe with SAS and RCS off: Ap 425 m lower, Pe 165 m lower. I'm quite sure I never saw that before 1.0.

Confirming phantom force. I noticed yesterday (with KSP 1.1.1) that in my old pre-1.0 save all my orbiting vessels seem to constantly slow down a bit. Ap and Pe decreasing around 0.1 m per second in Kerbin orbit and 0.1 m per 5 seconds in Duna orbit. Problem still there with 1.1.2 now. Turning on time warp makes Ap and Pe stable, turning time warp off makes both slowly decrease again. I'm going to try some other saves now. Installed mods: KER, Waypoint Manager, Kerbal Alarm Clock, KSP-AVC. Edit: Effect doesn't seem to depend on vessel mass, it looks exactly the same with a 16 ton vessel and a 165 ton vessel. And I noticed that Ap and Pe values don't change by the same rate all the time. The closer the vessel gets to either Ap or Pe, the faster I see the value for the closer point decrease while the other one goes down slower. Edit #2: Same problem when I start a new sandbox game and launch a small test rocket into stable orbit. Edit #3: Uninstalled KSP, removed all remaining folders from install location, reinstalled KSP, no mods, same results. So it's either the game itself or my computer forgot how to compute.