Could you try to set "Use Flat H.323 Dialling Plan When Routing Call" (TMS > Administrative Tools > Configuration > Conference Settings) to yes.
TMS Online help:
Use Flat H.323 Dialling Plan When Routing Calls
The Flat H.323 Dial Plan option is used to disable the Gatekeeper neighbor checking logic in call routing.
On: Configures Cisco TMS to assume a 'flat' dial plan, where all aliases can be dialed without prefixes no matter which Gatekeeper a device is registered to. When set to On, no Gatekeeper comparison is done in call routing. This is useful for situations where Cisco TMS is not managing the Gatekeepers so the neighbor checking can not be performed, or where Gatekeepers are not direct neighbors to each other (hierarchical or multi-legged paths).
Neighbor Zone prefixes read from Gatekeepers are not used in call routing when this option is set to On.
Off: Cisco TMS determines if gatekeepers are compatible by checking if the call participants are registered to the same gatekeeper or the gatekeepers are direct neighbors. Cisco TMS determines if an alias can be reached between gatekeepers and to insert E.164 dialing prefixes for neighbor zones if required by the gatekeeper's configuration. If Cisco TMS fails this neighbor check, it is assumed the call can not be made with H.323 aliases and alias options will not be given as a valid call routes.
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