Same here. Happened to me with the ion engines and both types of nuclear engines. So there is a possibility that TWR was < 0.1 but have to check to confirm
At the moment i just use the maneuver nodes to align my craft. As soon it is aligned i delete de maneuver and do the rest myself.
EDIT: With this method i was able to get everywhere i wanted so far (moons of Kerbin, Moho, Dres, Jool and its moons)
Encountered this as well. Even exited to KSC (which loads you back to Kerbin) to get into the tracking station again in hope the craft wouldn't be active anymore but nope... still wasn't able to accelerate time to a reasonable speed.
Had this one as well. Was working on a SSTO and at some point i wasn't able to load any craft to the runway/ramps at all. All attempts ended in an infinite loading screen. Simply restarting the game didn't work. The issue was permanent.
It also seemed like in the background anything was ready to go as i was able to stage with spacebar and hear the menu pop up when hitting escape.
To solve it i had to revert to an older save so i guess whatever caused it was also corrupting my save data