The only time I that I got a similar message

was when I brought my drive to friends and used it in their machine to transfer some files. Once I put the drive back in my machine I got the same "invalid system disk" message. I turned out that some of the system files (like io.sys) got messed up. The solution was quite simple though, I just had to boot with a floppy and type "sys c:" to transfer the proper system files back onto the c:\ drive. Your problem is probably different, but maybe this would work!