I had this problem too. I tried changing the fuser, the toner, the drum, and the print driver. No luck. BUT I GOT IT!
I replaced the big long padded roller that comes with the maintenance kit. That's the ticket.
Reverse the SCSI cable (Big thick one with the thumb screws that connects Printer-RIP) and see if it goes away, if it does, the cable is starting to go (or had a bad connection)
If the issue doesn't go away, either the RAM or HDD is starting to go, my guess would be RAM, but take my word on the "guess", it is only that.
Of course this all is only valid if it only happens to Fiery jobs, if it happens on copies, and only affects Black, then there is still a hardware thing, not sure what since you have replaced it all already though.
Having trouble with my xerox 560 printer with bustle EFI Fiery. Only printing half or less of the page. The machine does not flag an error, almost seems like the laser just stops writing momentarily on a printed page. I Have all new drums, new toner, new developer housings, new ibt assembly, new 2nd BTR. The prints are the same information. No variable data, no date information, it is almost a photo copy. We just run from the fiery to keep track of how many sets/books are printing. Any help would be great! I have three other machines that are not doing this!