Vinegar is produced by the fermentation of sugars (yeast uses an anaerobic process to break sugars down to ethanol), followed by exposure to air, and the bacterial breakdown of ethanol into vinegar. By these processes sugars in grapes, apples, rice, etc., are first converted to alcohol, and then allowed to “sour” into vinegar. Your problem sounds like you may have some fermented plant material in your ventilation system that is now turning into vinegar. The blower would send the smell throughout the car. (Or could it be that you have an old piece of fruit under the front seat?).
This sounds very much like a problem I’ve experienced on my current car here in the UK - an Alfa Romeo 156.
I was getting the same slightly acidic aroma when I first switched the blower on (with or without the A/C running) and so I took the car to an air condtitioning specialist (yes, such people exist in the UK - it soes occasionally get warm enough to warrant the need for cold air - blame global warming…).
The problem was fixed by having them service the ventilation system and with the addition of an anti-bacterial spray blown through, the smell was gone.
This was about 6 months ago and the A/C has had quite regular use throughout the summer months and so far, no nasty smells - I guess we’ll see how we go through the Winter.
Check the voltage regulator.
I had an Audi 100 and the voltage regulator was stuck on “charge”. The battery was overcharging and gradually bubbling away the battery acid, which caused a vinegar-like smell. When the battery acid was gone the voltage quickly ramped up (in about 30 seconds) and most of my lights and fuses burned out.
This could be dangerous if it happens at night, (as it did with me) so it should be checked out soon.
I was going to suggest that the smell might be coming as a result of using a silicon-based adhesive or sealant product in the ventilation system when the car was built (you get a strong vinegar smell when you open up a tube of silicon caulking, for example), but seeing as the car is a 2003 model, that doesn’t seem likely now.
My vote is with AnotherRay’s battery acid suggestion.
I don’t remember what the smell was like, but every now and then I’d get a whiff of something from my vents. Then I discovered my A/C evaporator had a leak. Once it was replaced, the smell was gone. Take it to an A/C shop. They’ve got electronic sniffers that will figure out if that’s the problem real quick. Good chance they’ll even do it for free. Just be sure to sit down before they give you the quote for fixing it.
One DIY that might be worth a try is to spray Lysol into the vents while it’s running. Start the car, crank up the A/C to full blast with outside air, then spray the stuff into the inlet on the outside just under the windshield. Wait for it to dissipate before getting back into the car. Anything that can kill germs on contact you don’t want in your lungs!