I just had this exact problem with my car. Fans running full speed for no reason. took it to VW dealer located near me, they said my fan control module was defective. They offered to repair it for $900 parts and labor. I told them I will do it myself for $300. I installed them myself, and to my surprise it didn't fix the problem. Called the dealer back to reschedule another diagnostic. They took my car and spoke with the tech in Germany only to find out the ECM went bad. I asked the how much this was going to cost, and this specific part they told me was on warranty for 150,000 miles or 12 years. Dealer ordered me a new one and kept my car overnight just in case the ECM didn't screw anything else up. Part was installed, and car works like new again. Also the dealer apologized for the miss diagnose and refunded me my $100. Now I either need to uninstall the new fans I bought, or sell my other ones.
I am not sure if every ECM is covered under this 150,000 mile warranty, but so glad mine was. You should check with them to make sure.
Just a quick note. I didn't tune my car so maybe that's why they replaced it for free.