Problems detecting different FPGA boards in the same machine

I ran into the same problem a while back when I had Terasic and a Bittware board on the same machine. The problem here is that every company forks Altera's reference PCI-E driver for themselves, and the driver will not work with another company's board. I don't think this problem will be ever addressed, unless Altera unifies all the drivers. Considering the fact the driver probably includes board-specific timing values, I am not sure if this is even possible to unify the drivers. Probably, your best bet is to write some bash script to perform all the necessary operations when you want to switch from one board to another. Or, you could put one of your boards in another machine (which is what I am doing right now).