I don't have an answer to your specific question, except to suggest that it could be almost anything really. Regardless, as you are likely thinking, this sounds like it may well be an inconvenient and/or costly repair.
Five years into its life, my 3800 developed an extremely recalcitrant clog that blew through $100 in wasted ink, and ultimately caused me to buy a 3880. With a rebate and a full supply of fresh ink, the pain wasn't too bad. The results are essentially the same, by the way, but that's fine by me since it's a great printer.
The anecdotal life-span of these printers seems to be about 5 years of typical use, so a replacement may indeed be a good idea. If you do replace it, remember that you can transfer over any unused ink except for vivid magenta, plus the dump tank.
Good luck.