I'm not familiar with this software, but similar apps (like Partition Magic) will give the same issue. I'd guess this is because you can't do a major change to the underlying file system whilst the disk is in use (by Windows etc.).
Partition Magic gets round this by allowing you to make a bootable floppy (which you can make into a bootable CD using Nero etc.) and running a barebones version from the floppy / CD (i.e. Windows not loaded).
Does Partition Manager have such a capability?