Hi Kishor,
We can try to help here first but it may be the type of problem that needs deeper research and thus a support case
It sounds like you are seeing some queues but not all? Please upload screenshots of what is visible in the Investigator and what is visible ion TIBCO EMS server
Referring to the documentation wiki
Monitor TIBCO Enterprise Message Service - CA Application Performance Management - 10.5 - CA Technologies Documentation
Does the agent user have permissions and correct confguration to access those missing queues?
Have you checked the agent log for any ERROR, WARN or exception messages?
Thanks
Lynn