Well, I replaced my fuse and everything seems to be right in the world again . I made a quick webpage that highlights the fuse replacement in the event that anyone else ever experiences this.

http://www.mrmunsell.com/EMPEG/Fuse_Replacement/fuse_replacement.html

Tony: Sorry for the late reply, I have been out of town. In answer to your question, I did maintain the inline fuse that comes in the EMPEG wire harness (this is the 3 Amp inline fuse in the main power line). I also have the factory fuses which protect both the switched and constant power lines.... so the main line is actually double fused. I have removed the accessories that used to share these fuses with the radio (lighter, etc), so I replaced the factory fuses with ones of lower current ratings to be safe (same rating as the EMPEG supplied fuse).

With all that said however, the EMPEG-supplied inline fuse has a 3 Amp rating (in my case anyway) while the mainboard fuse is a fast-acting 1 Amp fuse. So I would imagine that whatever caused this would always blow the mainboard fuse first due to it's much lower rating.