I had the same experience as bry99 a couple of weeks ago at IAH with CO Express. Waited in line (one person ahead of me) for the full service check-in since I wanted to check a bag and didn't like the looks of the longish e-ticket line for bag check since it was being served by a lone agent. Got up to the full-serve agent and she tells me that she "cannot" check me in because I have an e-ticket. I stare at her blankly and ask her why not. She states again that she "cannot" check me in due to my e-ticket - clearly no actual explanation was going to be forthcoming. I ask her "cannot or WILL not check me in?" She points me to the e-ticket machines (now with an even longer line of people) and refuses further discussion on the matter. Grumbling, I move to the other line and wait to check in at the machine - finally get up to the plate and the machine crashes and tells me to "please see a ticket agent." Fending off a complete meltdown, I sucked it up and went to another machine, completed my check-in and then settled in for the long wait in line to process my bag with the e-ticket agent. Total check in time (remembering that I was only originally behind one person to begin with) was 25 minutes. Then on to the security mess.
I was (and still am now that I write this) pissed off about this whole deal. CO's customer service continues to absolutely suck, especially compared to my alternate carrier, Delta.