I'm opening up my game (1.2) to see if I'm still experiencing this problem. My comment about 0.90 is just that it seemed like it was the golden age of mods. Other than reminiscing about the "good old days", totally unrelated to the current situation. Sorry for the confusion.
Last time I played, I was experiencing massive orbital decay at the Mun. Not so much at Kerbin, but my last launch attempt ended up falling back into the atmosphere due to this orbital decay, all the while my apoapsis was out by the Mun. Then, due to the extreme atmospheric drag of stock atmospheres, I got pulled back down pretty fast. Again, all the while my apoapsis was by the Mun. I'll post back here once I do some test runs.
Edit: My PE(73km)/AP(95km) is changing on its own around Kerbin. The PE starts moving ahead of the vessel (and getting lower), but it changes about once per second, not continuous. If I recall correctly, perhaps this is the issue of atmosphere extending beyond 70km?