I know this is not really a bug in Colloquy but rather a flaw in the IRC spec, but maybe Colloquy is able to cope with it...
I made a small list of what different networks have to say about the prefixes/modes they use:
holics: PREFIX=(qaohv)*-@%+ DreamIRCd-3.1.4-Phoenix
euirc: PREFIX=(qaohv)*!@%+ euIRCd1.1.5rc5
freenode: PREFIX=(ov)@+ hyperion-1.0.2
quakenet: PREFIX=(ov)@+ u2.10.11.07+asuka(1.2.1)
feki.de: PREFIX=(qaohv)~&@%+ Unreal3.2.4
Enterthegame: PREFIX=@+ bahamut-1.4(28)
notice how euIRC uses * for q and ! for a, while feki.de (my university server) uses & for a. Currently Colloquy interprets all of &, ! and * as Administrator/Protected (a), so on euIRC there is no difference between those two modes (both have the light pink super-op icon) while feki.de works just like you would expect it.
Maybe Colloquy could map the *!@%+ and ~&@%+ prefixes to the qaohv which are also provided and are the same for both networks. In that case of course you would have to watch for servers like EnterTheGame which don't provide this information (see #764).
I hope you understand what i mean O_o