This is probably going to sound weird (and after the four hours of hunting it took to figure out what in the hell was going on), I *believe* I've identified a bug with an unmatched quote in an inline comment breaking user-defined alias recognition. Normal doxygen commands continue to function as expected, but after the line of the unmatched quotation mark, all defined aliases stopped functioning. I tested *only* this change to confirm.

But first, some caveats; we're an LDMud coded in LPC, and we're running doxygen with our .c files aliased to java, as it's helped resolve some issues we've had with differences between C and LPC. The inline comment is reproduced below:

/* exit messages used to be printed here;
		Now, they're printed by the "exit_room_message function
		which is called in /obj/living/movement.c
		
		Done to resolve issues with exit messages printing, then
		player movement being stopped by a hook.
		Misery, November 2011*/

I can provide more information as needed, but hopefully this will be enough to reproduce the error as we've been able to reliably reproduce it in additional files. For reference:

Our only defined aliases are:
ALIASES                = "usage{1}=@par Usage:\n@code\n\1@endcode" \
                         "synopsis{1}=@par Synopsis:\n@code\n\1@endcode"

and a typical usage example is:

@usage{
	add_door(ROOM+"door1.c", ROOM+"door2.c");
	add_door(ROOM+"door2.c", ROOM+"door1.c");
}