Mocha for AE v. 2.1.0
Mac OS 10.6.8
I was doing an old tutorial on Mocha ("Gatorade" on Creative Cow) written in 2007. In it he goes to the file menu and choses RENDER to export twp mattes into after effects, he did not use Export Shape Data or Export Track data. In the tutorial a Render Wizard window opened up where he was able to choose which mattes to export. I know this is not an After Effects issue but since its Mocha for Ae I though I may be able to get a quick answer here.
You need a different version of Mocha. The CS4 version of Mocha exports the masks as data so you copy and paste onto a solid in AE. It's as easy as that.The end result is the same as exporting a matte in a version of Mocha that supports that.