I have just converted 429 clips into Cineform 3D avi, all aligned and ready to edit. Most of the clips were ouput through the timeline in PPro and some had to be stabilized and therefore output from After Effects. All clips were then muxed together in FirstLight.

All excited, I import the muxed 3D clips into PPro, everything plays back fine from the timeline. I export a 3D intermediate and find that some of the clips render as BLACK, if I had to guess, I'd say that the ones exported from After Effects are the culprits. I checked the metadata and some of them don't show the Hardware ID.

Any ideas?

Sorry, don;t know what that could be. Please put in a trouble ticket, Support Center (http://bit.ly/tticket) and also try are work out if it was a particular workflow that caused it (and repeatable.) You my also want to try the v5.3 b296 beta, many subtle 3D fixes.