Check the battery fuse box,, they are faulty and do not hold up to amps needed to run both fans when a/c is on... I had same problem and VW expert took a full 2 minutes to figure out since it's a very common problem... dealer only part, but you can replace it in 5 minutes... (if you look under fuses, you should see some partial melting of area where fuse contacts go in,,tell tale sign your box has failed)....
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WELL AC COMPRESSOR HAS TO BE WORKING IF YOU GETTING COLD AIR.YOU HAVE FUSE/RELAY BOX AT THE LEFT END OF THE INSTRUMENT PANEL ALSO YOU HAVE FUSE PANEL UNDER HOOD IN ENGINE COMPARTMENT ON TOP OF BATTERY.CHECK THE 30 AMP FUSES ONE CONTROL THE COOLANT FAN CONTROL MODULE IN WHICH OPERATES THE AC COMPRESSOR CLUTCH CIRCUIT AND AC PRESSURE SWITCH.
You would have to measure the pressure to determine if it's pressurized correctly. The compressor won't run if it's low. What happens when you push the a/c button? Can you hear/feel the compressor kick in? It seems like in most cases it's the compressor itself or the compressor clutch that goes. It's way too common in vw's...
Check the fuses under the hood for corroision. They should be locarted on the right hand side looking under the hood. I have a 2000 beetle that I was having problems with. technicans check everything and said all was o.k.. I found a fuse that was burnt up and cover with corroison. I cleaned the terminals replaced the fuse and have had no more problems.