In the video you posted the other day, from the 2003 AO, Federer was using a racquet that wasn't sold yet. They painted it like the Hyper ProStaff 6.1:

By Wimbledon, they were selling his racquet, and it was called the Pro Staff Tour 90:

Federer's racquet was slightly different from the ones sold in stores (the racquet was originally designed for Sampras) - the main difference was that Federer's had a slightly more open string pattern. By the time the KFactor was released, the production models had the same string pattern as Federer's racquet.
So the only one I would say was really a paint job was the one he used in early 2003 - they didn't sell his racquet, but they painted it like one they did sell. Since then, the racquet he used was the same as the ones sold, but his was just a modified version.
Most paint jobs are just a case of the pro using an older model, most likely the same one he used as a junior, and the manufacturer painting it to look like a current model. I don't expect the pros to switch frames every year, and I don't expect the manufacturer to pay them to endorse a model they no longer sell, so in most cases I don't see anything wrong with it.
The most shameless paint job that I know of is when Safin was playing with a "Dunlop" (2002 AO) - it was actually a Head Prestige with a Dunlop 100g paint job.
BTW: What do you mean the "new" ProStaff 85? do you mean the 88? Wilson hasn't made the 85 in years.