What exact Ae and Mocha? what are your footage specs? is this the exact same footage that was imported to mocha perfectly? or is this a different type of footage than before?
this could probably mean this footage codec is not fully supported by mocha and you have to export it to another format and import to mocha. it is recommended to use .mov files or image sequences for best results: https://www.imagineersystems.com/support/support-faq/#why-doesnt-mocha-support-my-footage
BTW imagineersystems lately released a mocha pro plugin: Plug-in Option « Imagineer Systems that sorts out this whole trasition between Ae and Mocha. with this plugin you don't have to deal with converting your footage if it's not supported format.
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I've actually sorted it now, It is all the same file types as I have been using and they are all .movs but the problem wasn't AE or Mocha, it was something wrong with QuickTime. I realised this when I couldn't open some renders that I have already opened. QT was telling me to install Apple App Support. Anyway long story short, uninstalled QT downloaded and re installed QT and now everything back to normal. Thanks for the help though.
Great! thanks for the update. this supports that the issue was a codec problem so re-installing fixed it.