HI @Joel_Fankam I would like to know something about your system to better understand.
Which kind of data do you get from your mocap system?
In which way, from this data, you form a message to send to /mavros/mocap/pose topic?
Anyway it could be a problem of reference frames and transformations between them. @LuckyBird explains very well the key concept to send the right messages with the right transformation for reference frame in his github repo and in his blog posts: