When you run a cleaning it doesn't really matter which black ink is active in the printer. You are cleaning the print heads and since the 3880 shares nozzles with both blacks this is not an area of concern. So long as the nozzle is firing and giving you a complete grid pattern it is okay.
Did you do a head alignment when you first set up the printer? If you didn't you should. Always use the auto alignment. Check pages 103-104 on how to do this in the manual. This is a good place to start troubleshooting a banding problem. Finally, the 3880 does not have the capability of switching from MK to PK and back again via the selection of Media Type or ICC paper profile. You must do the switch manually at the printer console.
Sometimes what may look like true banding (misfiring of nozzles) is actually head strikes. A head strike occurs when the carriage which moves the print heads horizontally strikes the paper. This is caused by paper that is curled or too thick. You can mitigate this by setting the platen gap to a wider setting and/or adjusting the paper thickness in the printer driver. Generally speaking when using most common Epson papers this is not necessary. I usually only have to make thee adjustments when using thicker and more rigid third party papers. If this issue persists I would contact Epson tech support since the printer is new. They will take care of it I assure you.
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