Thanks for the additional information Jesse.
Cartridges will not cause a printer to clean it's self more frequently, though I wouldn't rule out the possibility that Epson may program their printers to work differently/poorly with non-OEM carts installed... I know many customers who are happily using these carts with their printers auto cleaning/nozzle check both on and off, but we recommend using the manual control.
It would be great if other users would pitch in to share their experience with refill carts in a 7900/9900 or 7890/9890 printer, and if their using the auto or manual cleaning/nozzle checks.
It sounds like the carts are working correctly, and I've never heard of anyone having problems with our refill carts causing issues like you're experiencing, so suspect it may be a cleanliness issue, and recommend you 1. turn off the auto cleaning and nozzle checks, and 2. manually clean your printer's capping stations, wiper blade, and flushing box. It may also be good to gently clean the bottom of your print head. All these manual cleaning procedures can be found here: http://www.inkjetmall.com/tech/content.php?133-Printer-Cleaning-and-Preventative-Maintenance
I have no knowledge of the ink you're using, so that's part of the puzzle I can't troubleshoot/support.
I Hope this helps, keep me posted~ Dana