I think this desciption threw me off a little bit. I have been working with CIX Toshiba for a few years, but I don't use one on a daily bases. So when OP said that dialing 9 doesn't break dialtone, I thought "when did it ever break dialtone"? I always got a second dialtone after dialing 9. I checked with the Toshiba phone on my desk to be sure.

When dialing 9 for LCR, the Toshiba CIX will still provide a dialtone to the user. The dialtone will stop after the user dials the 1st digit of the phone number. As mentioned by Phonemeister, the entire phone number is sent to the PRI all at once when the user has completed dialing.
Does the provider require 11 digit dialing? I have been at several locations where the carrier requires 1 + area code but the users are dialing 10 digits, excluding the 1. I have also seen phone carriers prefer 10 digits without the 1, which meant that I had to strip the 1, and change the public dialing plan to 10 digits.
Also, check to see if they aren't using a pool line key or something to make a call. The should be dialing 9 from an Intercom key.