There were such issues with AE & mochaAE but these were solved with newer versions. A viable solution for you is not to have both apps running simultaneously. Then save mochaAE's tracking data to a text file. Exit mochaAE, start AE, copy the text file's content and paste onto the layer.
Intensive AE & Mocha Training in Singapore and Malaysia
Adobe ACE/ACI (version 7) & Imagineer Systems Inc Approved Mocha Trainer