I've been trying to figure out exactly what's causing it, but I have one specific garage door that will explode into many more pieces than what it was original built with when the door is opened from a recently (manually) closed state. When trying to close the door again, there is a large chunk missing from it. If I break the remaining doors and try to place blocks where the chunks broke off, it will refuse to place the block. Screenshots following.

It seems you can SOMETIMES recreate the problem by building a garage door and then placing a minecart track near it, but it's kind of hit-or-miss. In the world I'm playing in, the door will explode for no apparent reason, and in a test world the door exploded once when I put a rail next to it, and then acted normally subsequent times.

Have you tried the latest development build? The garage doors received a lot of attention that addresses most issues I found, including invalid drops.

Can confirm that this still occurs in 3.3.7 DEV.

It is difficult to say. If you happen to figure out how to reproduce the issue easily, let me know.

I've discovered the source of the problem. Turns out it was another mod called "Enviromine" which adds block physics, namely structures collapsing if not properly supported. For whatever reason, it was considering the garage doors to be unstable when opened (no blocks supporting under?) and causing them to technically fall like sand, which apparently freaks the garage door out and causes it to explode.

The fix for this was simply disabling physics on the garage door in the Enviromine config file. Sorry for wasting your time, I really should have come to this conclusion sooner.