Jon forwarded your email to me so I have a little more details about your situation.
The R3000 refill cartridges have an exit chamber that must be at least 1/2 filled with ink for proper ink flow from the cartridge into your printer. As per our instructions, the cartridges must be vacuum filled in order to get ink in the exit chamber for proper function. Since you didn't vacuum fill the cartridge, there was no ink in the exit chamber when you installed the cart into your printer, so printing and cleaning cycles have used the ink in the printer's internal ink line and drawn in air since the cart wasn't filled correctly, and the air is interrupting the ink flow. To remedy this situation, you will need to remove and refill the cartridge via the vacuum method, by plugging the air vent hole and drawing a vacuum with the filling syringe to have ink drawn into the exit chamber. Open the air vent hole after vacuum filling the cart, then tap exit valve down on a folded paper towel a few times to force ink down and air up, then install the cart into your printer so it snaps in for a good fit.
After reinstalling the cartridge that has been vacuum filed with ink in the exit chamber, you will need to purge air and get the ink line filled with ink again for consistent flow. There are two ways you can do this:
1. Using the Adjustment Program (which you can get from www.2manuals.com), run the Ink Fill cycle
2. Using QuadTone RIP, following our instructions for printing with Calibration Mode to purge the individual channel (instructions can be found here: http://www.inkjetmall.com/tech/content.php?144-Print-Ink-Separation-Image-thru-QTR-Calibration-Mode)
Please be sure to thoroughly read and follow the refill cartridge instructions for the best results and to avoid issues like this.
I hope this helps. Please let me know if you have further questions or if there's anything else I can help you with.
Best regards~ Dana