Uninteded decrease of orbit around kerbin (above 70km)

[NASAHireMe]

My guess would not be phantom impulse due to part clipping. My guess would be a 'random acceleration' bug.

I've been playing KSP for 6 months now, visited and landed on all the bodies, captured asteroids, etc. In the course of those 6 months, I've encountered the 'random acceleration' bug probably five or six times now (all in KSP v.0.25 or before).

If my memory serves me, each case of that bug occurred when I had a spacecraft with the Klaw. This is probably the most well-known bug in the game; seriously, just Google "Kerbal random acceleration" or "Kerbal phantom forces" and you'll see many reports of the Klaw. The Klaw is notorious for producing this bug.

I haven't upgraded to 0.90 yet; I'm still playing 0.25. So I don't know if they fixed the Klaw problem in 0.90. And since your craft doesn't appear to have the Klaw, maybe you've stumbled into a new bug that is unique to 0.90. But it appears to be the same bug as the old Klaw bug, except no Klaw (obviously). To fix the Klaw bug, you had to simply revert to an earlier savefile, relaunch and rebuild the spacecraft, and hope that the bug wouldn't hit you the second time around. Maybe you should try the same, and see if building and launching the exact same spacecraft produces the phantom acceleration you posted about originally.