I'm sorry to hear of your experience, and will try my best to help resolve this issue to get you back to happily printing.
Maintenance is important to keep the printer clean and in good working condition (this is true with any machine), but if everything was working well after you first installed the carts and did a few test prints, then I don't see the need for flushing the print head, and believe you may have caused the problem during the cleaning process somehow... We recommend cleaning the printer's capping station and wiper blade on a regular basis (every few weeks) to keep the head clean and in good working condition, and if you experience stubborn clogged nozzles, dripping or smears on the paper, then gently clean the bottom of the print head, and carefully flush the print head using our print head cleaning kit. If your printer is working well and all channels are fully printing on the nozzle check, there's no need to flush the print head.
It would be helpful to see a photo of your nozzle check. Please read instructions on how to attach files to this forum, here: http://www.inkjetmall.com/tech/content.php?152-How-to-attach-images-to-this-forum
Was there excess fluid in the bottom of the cartridge chamber, and/or did the paper towel get overly saturated when you flushed the print head?
How much PiezoFlush did you inject thru each channel of the print head?
Did you inspect paper towels after removing from under the print head, to make sure they were fully intact, and a piece of paper towel didn't rip off?
Did you overflow the capping station, or did any fluid drip into the printer body while cleaning the capping station?
Did you clean the bottom of the print head after using the print head cleaning kit, as per our instructions?
If you flooded the head or electrical areas of the printer while cleaning your printer, it could cause strange things to happen, like what you're experiencing. If this is what's going on, it may work fine after drying out for a few days, though in extreme head flooding situations where nothing was printing due to wet electrical, gently removing the head, and disconnecting the ribbon cable, then carefully drying the cable and connection areas with Q-tips, and reconnecting, has resolved the issue for the few customers who have done this.
If you have paper towel stuck to the bottom of the head, then I recommend carefully cleaning the bottom of the print head and wiper blade, following our instructions, here: http://www.inkjetmall.com/tech/content.php?133-Printer-Cleaning-and-Preventative-Maintenance
Another thought is the encoder strip, which is a thin clear plastic strip that extends the length of the printer, and has tiny lines on it, which is how the print head knows where it is. If the encoder strip became disconnected, or is dirty with ink, then the printer will act strangely. Check to make sure the encoder strip is correctly attached, and isn't dirty. If it is dirty, use an alcohol pad to clean it by opening the pad and gently pinching the strip between the opened pad (so it's folded over the strip, to clean both sides), and carefully wipe the strip from one side to the other (try to use a smooth motion, not scrubbing it back and forth).
I hope this helps.
Please keep me posted, and let me know if you have questions or there's anything else I can help you with.