InDesign doesn't make the Page Setup dialog.
What kind of printer are you printing to? It sounds like could be a printer driver issue. Have you checked for updates with your printer vendor?
I'm printing to a Konica Minolta Bizhub Press C1060. The driver isn't 100% Compatible, there are a few issues I've had with it so far, but this one is new. The thing that confuses me most about it is I have another computer also running Yosemite, printing to the same printer and using the same driver, and when I look under page setup, it shows "Other" and the correct dimensions. The issue is only happening on our brand new iMac we got this past weekend.
It seems that the print driver is getting the size from the system page setup, and not Indesign's document setup.