So I had the alternator replaced under warranty (still had to pay a $113 deductable!!) and ever since the fogs don't turn on, all fuses are good, could it be a relay? All other lights, including high beams work fine. Also, since I had the car returned the aftermarket deck lights are always on when the car's running and the headlight switch is on (any position), regardless of the deck being turned "off", this used to never happen. Whenever the head unit was turned off, all it's lights would go out.
Any ideas?
Seems like they spliced and diced your wiring system to solve a problem they couldn't figure out and place the blame on you for having a AF deck. So I figure when they were splicing in the dim lights on the deck they f'd up some where and must have bypassed a relay, and probably didn't crimp or sodder the wire for the fog light properly. Thats all i can figure out, Good luck.
First, I would check the wiring from your fogs, maybe they undid the loom to get at the alternator. It could be the relay; you have checked that your high beams aren't on, right?
That said, you should go right away (assuming they're factory foglights) back to the dealer -- they can check and fix it under the last claim without having to pay the deductible, especially since the change seemed to coincide with the work they did.
As for the deck, I'm betting that it's a setting somewhere in the deck that got reset to default when they disconnected your battery. I used to have a Pioneer deck that had settings you put in when the deck was off -- for example, whether you wanted the clock on all the time or just when the deck was on. On that deck you had to have the ignition on, the deck off, push and hold the function key until the menu came up. There was a bunch of settings like selecting subwoofer type, clock, etc.