Hi
I am not sure what has already been done in the troubleshooting line so unless we can narrow it down even more it can be quite a few different causes to this. It is nice to know which exact endpoint models are being used and which software version the nodes are running and what protocol you are calling on? Are you calling on the same protocol to the MCU as you do direct? Are they registered to CUCM or VCS?
Then start at the basics, are the MCU conference muting the participants automatically? Are the far-end muted or vice versa? Is the MCU working with audio & video internally? Was it working before for external participants? What is the difference?
If this is not the problem then you should start looking into logs and maybe take a packet capture to see what is negotiated between the MCU and the endpoint. The logging options are many so it will help by knowing the software version and endpoint model.
If you need assistance with these logs it might be wise to open a TAC case if this is not a simple case.
/Magnus