What CS6 suite did you install? Certain suites and products install a limited list of export formats for AME, for example Flash Pro or the Design & Web suite. If you have Premiere CS6 you should have a full list of exporters tho', including MPEG-2. If that's the case, make sure you also update Premiere to 6.0.1.
If uninstalling and reinstalling CS6 doesn't work, you may want to check if there are any pre-release versions of Adobe products on your system and uninstall those, and also try running these cleaning scripts.
BTW, other users have reported problems with missing exporters, here one thread with a workaround that has helped...
I installed master collection. I did run the updater for 6.0.1 for both PP and AME and neither still have the Mpeg-2 codec. What's odd, is AME does have presets for DVD output, but when I try to drag that preset, I get an error. I also tried to create a custom output, but there's no Mpeg-2 codec to choose from. I did some searching around the 'contents' of the app and found an Mpeg-2 exporter in a folder with all the others, but for some reason when both PP and AME boots, they don't load the codec.
there aren't any pre-release versions of the software that I can tell, but I suppose anything is possible.
I looked into the thread you posted, but didn't have much help relating to missing or non-loading codecs. I'd prefer not to uninstall and reinstall if I can help it. I have a big transcode job that I was hoping to run with AME but looks like Apple Compressor will have to do.
One easier step to try before uninstall and re-install is to deactivate (under help menu) PPro, reboot the system, launch PPro again, it won't let you in most likely, start AME which will also probably not launch because of deactivation. Now reboot machine again, go back into PPro, re-activate PPro with your serial number, close PPro and start AME. check both and see if missing MPEG2 codec is there now. This is obviously licensing issue. AME is dependent on PPro or suite for its licensing . So I'm hoping that deactivating and re-activating PPro will resolve this issue.
Requesting the users who are facing this problem to please help us by mailing the amt3.log and oobelib.log form your /tmp folder (mac) or %temp% folder (win).
Please mail it to email@example.com since its difficult to view it on a forum.