Dear Arpa,
The issue could be related to the signal structure used to load the input signal to the Matlab component and transfer the output signal out of the Matlab component to other components. You may check the examples in OptiSystem Example Library located at the following link for more information and guidance.
You may send your Matlab code used in the component and OptiSystem project as zip file to check it. My email is ahmad.atieh@optiwave.com
Which version of OptiSystem are you using?
C:\Users\USER NAME\Documents\OptiSystem 17.1 Samples\Software interworking\MATLAB co-simulation
Regards,
Ahmad