After entering (non-physics) timewarp, and then either increasing timewarp once (doesn't happen with further timewarp increases), or leaving timewarp and returning to normal speed, the game stutters/freezes for a short period; the period of time that the game freezes when this happens seems to be proportional to number of engines/parts on ship (regardless of whether of not they have Background Thrust enabled).
Version 1.12.5 (can provide mod list if needed)
When entering and leaving timewarp background thrust has to create a bunch of part resources for the warp buffer. That's the cause of the stuttering you're seeing. There's likely something I can do to improve things though. I'll take a look when I get a chance.
Worst case I can make this a one-time thing so that you only get the stutter once instead of every time you enter/leave time warp.