You should be able to format the Linux partitions from within Windows. I don't have Windows on my compy so I can't check which program you need but I think it's one of the system tools (even though Windows probably won't let you see the partitions as 'd', 'e' drives etc) otherwise you could insert your Windows install cd and format the Linux partitions as NTFS / FAT32 with that (then abort the process so you don't end up installing Windows again) or boot up a Linux cd and format the space as FAT32 that way.