Re:Now (Score 1)

From what I've heard it seems to be a problem mainly with dual boot where you have each OS on a separate drive, rather than both on the same partitioned drive.

Actually, it's quite the opposite:the problem appears when both OSes share the same drive. FC2 installer tries to fix the faulty partition table generated by Windows. The situation is different when each OS is on a separate drive. I have this kind of setup and I haven't experienced any problems.