I had a usb cable that worked for years with my Prophet 6 not work with my Pro 3. It still works with my Prophet 6, and I thought I had an issue with my Pro 3, but after trying a couple more cables one of them that's almost brand new works with both instruments every time perfectly.
I know it seems ridiculous, but I'd try a new usb cable, even if your cable works with other instruments. It worked for me.