Inkjet printer self alignment issue

I'm kind of curious about this I've had this printer a few months now. The local college was tossing it I assume because this alignmenterror.

It is an HP Officejet 6500 all in one. When you power it on it automatically prints an alignment page. It then says alignment failure press okay. It prints black fine and the level gages say black is near full. The 3 color cartridge just show a ? and don't print in color. I tried taking out the cartridges and running an eraser on the contacts as well as the carage contacts and nothing.

I'm kind of curious if maybe the issue is just empty or faulty color cartridges and the color failing to print messes up the alignment. I'm not totally sure how it works but I can see a red light at times during alignment if look in the paper output.

Has anyone seen this before? Does color matter in the alignment...