OK, I figured it out (I’m pretty sure) and I was able to replicate the bug.
This is totally what is happening:
It seems like the transition directly from Take Slack → Running the file is causing the machine to freak out and think it’s in the wrong place so it goes into safe mode.
The short term fix is that if you use the arrow buttons to move it around IE:
Retract All → Extend All → Hook Belts Up → Take Slack → Move with the arrow buttons (100mm left, 100mm right or something) → Green Play
I guess I had never tried starting a file immediately after doing Take Slack (I always re-positioned first), thanks for catching that. I will get that bug fixed right away.
In the mean time here’s an update which will at least give a more clear error message about what is going on: 0.66.4