Eureka! I think I'm onto the problem, partially my fault and partially the shops fault.
In the past, I'd been asked to do my own seps before sending jobs to the shop, so I'd output each spot color to it's own PDF. This would put all the color info into the black channel of the PDF, leaving the C, M, & Y channels empty. At that point, they'd assign each PDF to a different print head and run them whole, like any other office document. Their press only has two, so they can't run 4-color process jobs and we're only talking about two PDFs. After reading your responses, this is clearly Neanderthal, but it's worked for as long as I've been here.
Since then, the shop has a new manager and it appears he's been trying to separate my separations. Since he kept telling me I was sending 4-color files I'm not sure why it didn't ocurr to me sooner. Since all PDFs have CMYK channels, he's been seeing that and thinking they are four color jobs, even though all the color info is on one plate. My solution so far is to upgrade my export format to PDF/X-4 and have him do his own separations. I sent a test file and he said he "was able to make it work", though he still complained about the CMYK channels. I've explained to him that all PDFs will have CMYK channels and that a two-color job will separate as four empty CMYK plates plus two plates for the spot colors.
Does this sound about right, or am I still missing some part of the picture? I feel like Buck Rogers waking up in the 23rd Century. Where the hell have I been all this time? Oh, yeah - civil service. Gotta get outta this place!