Transpac,
I've never had UA reservations trouble me over this before... I've got a SYD-SFO flight booked in 2004 and they went ahead and cleared the upgrade. As someone mentioned earlier, the threat of them putting you back in 59E between the fat guy and the screaming six-year-old should be sufficient motivation to make sure that you actually have an upgrade to use when your flight comes around. ;-) I'd try calling back and maybe someone else will help you, or you can explain the above rationale to them and maybe that will help.
--lj