My oldest N900 needed a reflash again recently, and it too had this error (the N900 in question stopped being my only/primary device precisely because of the telephony-functions-disabled error) - anyway, I had this error too (that, or alternatively, on a few attempts I got other more obscure CMT related errors), and after a bunch of attempts to reflash it that way, I gave up, and then next thing I know a few minutes later it booted up again, working fine. Perhaps it's possible that you don't actually need the CMT flashing part to succeed, and the rest of the flash already gets done before the flasher fails due to CMT error(s)?

*Shrug* Worth some more testing.