Claw

Yes. The parts act like a big tree (as mentioned earlier). If there's a loop, the physics calculations break.
 
Nope. They automatically disconnect with no action needed on your part (which is why I prefer it over the auto-strut, which can sometimes have unintended consequences).
 
Cool. Just wanted to make sure (it's a common thing for people to try and get tripped up on). Glad you're already on top of it!
 
Also, welcome to the forums!
 

Everyone usually just calls me Claw.
I'll see if the curly braces doom my save here.

Please see here. We'll need logs and other info to help troubleshoot.
Thanks
 

I've located the bug. If you aren't opposed to add-ons, I've added the fix to my StockBugFixes.
With the stock bug fixes, you can continue using Physics.cfg normally (no need to lock it read-only or delete anything). The particular bug fix module is called "BodyLiftFix" and is actually purely standalone (StockPlus not required). If you want, you can delete everything else in the download (which is contrary to the install readme, but still possible for this particular module...not so for the other modules).
The only "pure stock" way to avoid this is to do the read-only tricks outlined above, or delete physics.cfg every time you start the game.
Cheers,
~Claw

Yes indeed, it's a bug with the CoL on the fairings (as also described here). Unfortunately it's not an edge case, and beware that the aero markers lie to you after jettisoning the fairing (until you cycle the overlay).
Not that I like saying "there's a mod for that," but if you aren't opposed to addons, I've fixed this in the latest release of bug fixes.
Otherwise the only "workaround" is to not use fairings, or design the craft in such a way as to still be controllable with a lever arm that far up.
Cheers,
~Claw