This is certainly very strange! The orange and yellow positions aren't paired, so the two couldn't mix in the damper or capping station.
From what I can see, the orange position is printing faint yellow on your nozzle check, which I have never seen or heard of happening before. The ink is clearly orange from the photo you sent of your carts...
Did you make sure to shake ink bottles before filling/refilling carts?
Although I can't see fine detail because of image resolution, I did enlarge your nozzle check scan and see several channels have many mis-firing nozzles.
Considering the things that could possibly cause what you're experiencing:
1. I wouldn't think build up in the damper would evenly filter the orange ink to make it print faint yellow without causing significant ink flow troubles and missing nozzles.
2. The print head couldn't have back pressure and suck up yellow ink into the orange channel, because the two channels aren't paired (Y is paired with LLK, and OR is paired with GR).
3. Due to mis-firing nozzles in other channels, I believe your printer needs some manual cleaning and/or the environmental conditions aren't correct, but a dirty printer or incorrect temp or humidity levels wouldn't change the color of an ink, but more likely would cause ink flow issues such as clogging and mis-firing nozzles.
4. Electrical: bad signal that's making the printer use the yellow channel instead of orange- but if this were the case, I would suspect it would print the same as the yellow channel, not lighter...
5. Altered Ink Separation image, though this wouldn't explain why the nozzle check is printing light yellow...
Have you tried shutting down both the computer and printer, then at startup, uninstall the 9900 print driver, then download and install the current driver from the Epson site? I have experienced overall very light output with our 9880s occasionally when the computer has been plugged into a different printer, then back, which is fixed by reinstalling the print driver.
Aside from your light yellow printing orange channel, I recommend manually cleaning your printer's capping station, wiper blade and bottom of the print head, and checking the temp/humidity levels in your printing environment to help other channels print fully/clean. We have helpful cleaning/maintenance tips available here: http://www.inkjetmall.com/tech/content.php?133-Printer-Cleaning-and-Preventative-Maintenance
I hope this helps, pleas keep me posted, and let me know what you discover, if you have further questions or there's anything else I can help you with.
Best regards~ Dana