Couple of things:
Mocha Temp/Cache does not update consistently. Deleted Temp Folder altogether because there was no temp data cached. New Layer in AE is no help either. Solution: Create a new Mocha File, delete the temp folder and track again.
Track in Mocha AE looks excellent. Upon import [with Alt Tab] about 10-15% of the keyframes are WAY off.
FYI: I am ONLY TRACKING 36 Frames.
What can be the issue? ANY assistance will help.
When you paste or import your mocha data into the final composite or edit, make sure you are pasting or loading your data in at the first frame of the clip, otherwise your data will not line up.
Project settings such as frame rate, dimensions and pixel aspect ratio must be match between your mocha project and your destination software. Make sure these values match the settings in your compositor or editor and inside of mocha, otherwise your tracking data will not match when you export it.
If your are using Adobe After Effects, the target layer you are pasting data to should also be the same size as your AE composition. A good After Effects troubleshooting tip: create a new solid that is the same size as your composition. Paste your track or roto shape data to this layer. If it does not line up, the issue is mostly likely a project mismatch.
Can you check that and see if it fixes your issue?