Matlab does not seem to retrieve all the data points from Vicon's frame?

I am currently trying to process EMG data(3000Hz) real-time using Matlab. I have utilised the Vicon Datastream SDK to retrieve data from Vicon(500Hz) to Matlab.

I have a trigger point, and when this point is triggered Matlab would then retreive x-amount of data from vicon. However, when this is carried out real-time, Matlab has a difficulty detecting the trigger point(Square Pulse). Sometimes it would detect the trigger point but the EMG data does not seemed to be fully collected as the response I am looking for is not visible where it is visible on Vicon Nexcus.

On the other hand, if the process was carried out in offline by going through frame by frame then Matlab is able to detect the trigger signal which then retreives EMG data correctly.

Any comments will be helpful!

Thanks!