I had a much nicer licensing audit that a lot of people I imagine. I was terrified of being audited as I was SURE we were out of compliance but thought when an audit came through, they would catch it. I had brought it up to my supervisor that my interpretation of the licensing terms meant we were violating them, but he said not to worry as we will likely get audited at some point and we are doing our best to be within the licensing terms.
Then the day came of the audit and I was sure I'd be having to explain a bunch of things to the Microsoft Licensing auditor and praying I could talk my way out of it. They sent the IT manager a tool to run which connected to AD and then scraped the network to make sure we had no rogue computers. Then it did a software audit on the machines and packaged it up to send back to Microsoft. Microsoft reviewed it and reviewed what we were licensed for and sent an email back to the IT manager with their observations and asked us to explain a few things.
Most of what they found was easy to explain - our test blades had test versions of SQL installed licensed under MSDN. That one was easy. This also covered our test SSIS and test SSRS servers. So far so good... but then they found our SSRS server. A server which was created ONLY to host SSRS (created before I started, and at this point I was a good 6 years into being a DBA, so the server was likely close to 10 years old). Microsoft told us we needed to move SSRS onto a server licensed with SQL Server OR buy an additional SQL Server license. That was it. No back pay on licensing for 10 years, no fines for running it ulicensed... just a "please move the server or buy a license". At that time, I was not aware that SSRS needed to be on a licensed SQL Server machine. Did not understand that as SSRS requires a SQL Server back end, so I thought it would be more like SSMS. Learned something that day. Well, learned 2 things - also learned how to move SSRS to a new server without losing any reports! I had read how to do it, but had never actually done it at that point.
We also had to buy a few more Office licenses and Windows licenses for desktops, but overall, the Microsoft audit was a lot of stress for nothing.
As long as we are TRYING to meet the spirit of the license, Microsoft seems to be pretty reasonable. The thing to remember is if they come down too hard on you, they may lose you as a customer. If the audit is too intrusive, they may lose you as a customer. The company doing the audit wants to make money off of you, so they are going to do what they can to keep you happy while making money.