Sydupe seems to be a Sytel edit, is that right Chuck?
Nope, it was a Sydex tool. And it's useful only if you have more than one FDC, mapped to a different I/O port, IRQ and DMA. That's not very comon. Much less a system with more than 2 floppy drives connected to those controllers. The configuration was large enough to support up to 12 floppy drives at once. I think one of our customers set up two tower cases, with the second one holding only drives.
Somewhere on this forum, I posted another formatting program, ConFormat that runs in the background (popup window). It was popular before GUIs. Otherwise, nothing out of the ordinary.
I wonder if your 5.25" disks are high-density when you're trying to format them as low, or vice-versa.