Is your usb cable plugged directly into the Mac or are you using a usb hub? For some, hubs cause problems with connecting to outboard equipment.
I had a similar problem with a Korg Prologue last year. At first my Mac and it talked to each other and then ... not, for no apparent reason. My solution was to do the updates with a Windows laptop. At least, with the Prophet you have the option of updating via the midi port, as studiodc suggested. This is the way I do it.
Keith