Cannot warp, revert or save mission in progress- possible issue with BetterTimeWarp? And DSEV question

[MrBonesWildRide]

So I'm trying to build a three part interplanetary ship with a nuclear / fusion laser engine and I have two problems. First, I have the first two stages in orbit, but every time I try to launch the engine itself, once I get into orbit, both using MechJeb and manually flying the parts, the game says that the ship is under acceleration, preventing me from setting up a time friendly rendezvous with the target vessel! Also, since KSP thinks the craft is under acceleration, I cannot revert or go back to the KSC without losing the launch!

I'm certain this issue is with either BetterTimeWarp, the cruise control enable nuke/fusion engines from Deep Space Exploration Vehicles, or MechJeb. I've never used engines like these in KSP so I'm not 100% how to use them correctly, and I couldn't find a guide/tutorial on how they work. All of these and the other mods I have were installed and have been kept updated by CKAN. Here is my player log:

Player.log