Joe, I didn't take it that way, just wanted to state for the record that we use that temperature and thus far haven't had a problem with it.
As for your problem... I'm not sure what to tell you. Perhaps they're being heated for too long? My numbers are suggestions. I don't actually set a time, I just keep watching, then feeling the liner to figure out when to pull it out of the heat.
For the cuff height being different, I've only seen that when one has been pulled too much. I give the liner a gentle tug before tightening the buckles and I don't tighten the buckles very tight. Sometimes when the buckles are cinched down too much, the liner is pushed upward.
For the short sole, I've never seen that! That's very strange. Does it shorten while your foot is in the boot cooling the liner or post cooling when your foot is out?
Something that does come to mind... I've never molded an INTUITION without an orthotic/footbed on the person's foot. Maybe I've just been lucky and not witnessed this problem.