Charging question
 

1999 A6 A little advice here...I noticed today my battery light was on and the gauge showed I was only pulling 12 volts, far from the consistent 14 I usually have. Stopped and had the battery tested first...device said I had a bad battery (it was almost 5 years old and survived many a cold day). I put a new one in, had the tech retest to check on the alternator as well- test said I was fine. An hour later I notice that light was back on, went the back to the battery dealer, and after some consultation it was decided that maybe it was a bad new battery. Threw another new one in, and now I get 12 volts on the gauge, the tester says I'm at 65% and we can't really check to see if the alternator is actually OK...oh, and I've got a check engine light that goes and comes..

does any of this sound familiar, something specific for an Audi, outside of potential normal charging problems?

Replace the voltage regulator in the alternator. It usually mounted on the back of the unit. The brushes have probably worn down and not making good contact with the stator in the alternator. Easy replacement. Bosch alternators are usually about bulletproof but the voltage regulator is usually the culprit when your having charging problems.

99 1999 Audi A6 Quattro Voltage Regulator - Engine Electrical - Beru - PartsGeek

This morning I needed a jump- not enough to start obviously..then it was 14volts most of the day...now it's hovering around 12volts..another weird thing, the instant up or down feature of the windows isn't working, but the windows do if the switch is held down? possibly related?

If the battery discharges enough, the mode of the window switches goes back to the default mode that performs like you are experiencing. I can't remember off the top of my head but there is a button sequence you have to press to get the auto up and down mode back. It's in the owners manual in the power windows section.

I'd still replace the voltage regulator. Sometimes when the brushes get worn down, they will make contact periodically but it never lasts long enough to properly keep the battery charged. If you're seeing 14volts, it is at maximum charge which will usually occur when the battery gets below a certain point. Normal charging should be around 12.5 to 13.5 volts.