Ah okay great. I'm not crazy. Below is a more simplified example of a different ship I made for the purpose of figuring this out. Just a command pod with a liquid engine on the bottom to bump it away from the pad (apparently the timers don't start until after you leave the pad; makes sense). I never left the vessel, just time warped until it ran out (I did leave the vessel in the case of the original Mun Orbit ship, but apparently it doesn't matter).
I have the save file, but I'm note sure how to upload it.
I also added a gamedata screenshot.
Thank you!