I did confirm Tones are correct once again and I do have in my files that tone A is .6 Sec and Tone B is 2 Sec. however I still do not see where I can change that in Quick Call or under Tone Signal tab without selecting Singletone.
I'm gonna throw something out there that might be totally out in left field-
MDC/QCII= is this also using PL or DPL on the channel? if so, are u able to hear the tones when on the channel as they come over the air? If yes, IDK what the issue is, if no, Radio is receiving the tones, but the decoder isn't getting them due to the audio technically being squelched. Some systems using PL won't drop the PL on transmit for paging but the original standard had the PL dropped on transmit for paging from the console side.
Otherwise, contact your radio shop, dispatch center, etc to have them take a look at it. Since you have the MDC/QCII firmware- it is possible u have one of the "flaky" versions. Initial deployment of that option with testing by City of Pittsburgh/Allegheny County one of the versions released during testing (that were also regular deployment) had issues with certain tones. Might want to load latest version of firmware.