If the cap is "on the -12V rail" that means the cap's positive terminal is connected to the 0V reference level ("ground") and the cap's negative terminal is connected to the -12V supply. Right so far?
So if you just put your DMM across the cap, with the DMM's positive lead to the cap's positive terminal and the DMM's negative lead to the cap's negative terminal, you will read +12V, since the circuit's 0V reference level is 12 volts above the -12V rail. Right?
So what seems to be the problem?