My 3516 is missing some lines in the same places when printing B&W and also is not able to complete the alignment process when it scans in the alignment page, however the alignment page does look fine and doesnt appear to be missing anything on the page.
I then did the usual printer head cleaning process various times, changed the cartridges for new ones, and even cleaned the contacts within the printer itself with alcohol and printed the print quality diagnostics report and it has failed one item which is the alignment status.
I managed to resolve it in the end. Paper in the upright feed was aligned to the far left, aligning it to the far right allowed it to print the alignment sheet centralized and then it was able to correctly scan and self align.
I have another question, after a few years should the printer be serviced/cleaned in order to keep it running for as long as possible?