When I tried to protect an unprotected map called StarQuest (haha), when I tried to play it in game, it worked all until the briefing, but after everyone pressed start, the game crashed out. For everyone. Does anyone else experience this, or is this a unique game issue?

yes
http://www.staredit.net/topic/6881/

I've heard of several protectors crashing Macs in breifings and such, I'm sure this is a similar problem, just try another protector.

My computer... is a PC... It crashes when the game starts... the Briefing works fine...

And Shadow can be unprotected by UU2.

I would recommend compression then, give up on completely protecting your map.

Post the crash log found in your Starcraft's Errors folder.

If the original maker intended the map to be open source then you shouldn't be protecting it any way.