With my town, I had 3 Arcane Studies built, but the town info box and the town report both indicated that I was only getting the research bonus from 2 of them and my research buffing champ (totaled to 2.4 I think). I built another Arcane Study (it said it would take 0 turns to build) and the town text didn't change. I advanced the turn to see if it would register then, but still no dice. Town research was still 2.4. I demolished the 4th Arcane study and tried building other things. Everything I tried that would take 0 turns (or '-1' turns) to build had the same prob.

A bit later, I got the Civilization tech to build libraries and my Arcane Studies all upgraded to Libraries (the graphic for the library isn't centered on the tile correctly, btw). Now my town text read that I was getting 6.8 research points, so that 3rd Arcane Study/Library was suddenly working, but again, new Libraries wouldn't work.