I have a layer in AE. I have set a work region. Send the clip to Mocha via the plugin, it’s coming up short on frames. I have no idea why. Anything?
Try precomping it, moving all attributes into the new comp, and then trimming the comp to the work area. Then put Mocha on the Precomp and see if it still happens. I am not sure what is going on, but that kind of thing can usually fix weird issues with footage.