That's just too weird. I've never seen anything like that unless, as I said, there are no FAT partitions available and Windows has to make one somehow.

I partition all my boxes with either a primary FAT or NTFS partition first for Windows to live on, then a primary Linux swap, and a big extended partition that holds all my Linux and BSD stuff. Windows has never complained beyond popping up a dialog to let me know that it has detected non-FAT partitions. It has never halted the install or refused to allow me to continue. The only possibility I can think of is that Linux might be on a primary partition that's marked as active and Windows can't see its own partition. Other than that, I'm at a complete loss.

But I'm 100% sure that I'm right about this. I've done it too many times. But just to be sure I'm not losing my mind, I'm going to pull out one of my boxes I'm not using at the moment and test it. I'll post the specifics and the results in a day or two after I've had time to get around to it.