Strange Fat32

I had a motherboard which couldn’t recognize hard disks > 8Go. When I bought one (IBM) 14Go, I formatted it with the patch to recognize it. It resulted a Fat32 system which cannot be recognized under dos (floppy boot) unless a particular operation (press space bar before reading a floppy otherwise the HD will not be recognized).
Now, I have an Athlon. I would like to convert the Fat into a classic Fat32 file system without reformatting it (too many data). I don’t want to see this blue message each time I boot!
How could I do that?

Thanks.