Your right to look at the Tones key.
I would suspect that the problem is that the button labeled on the keypad as "tones" isn't really tones.
Go into your options and edit the keypad and take a look at it.
The way it needs to work is, the operator has a call on the line, dials VM, VM answers, operator presses the "tones" key and then dials the codes she needs to.
Hope that helps.
Ralph