See this similar thread...
Not sure this workaround will help in your case, but you may want to try replacing the following file in the AME CS6 package bundle with one from another Mac that doesn't have the problem:
/Applications/Adobe Media Encoder CS6/Adobe Media Encoder CS6.app/Contents/Resources/txt/AddExporterList.txt
If you don't have another Mac system with CS6 installed just email me and I'll send you a copy from mine. If this doesn't help we might need to do some spelunking to track down what's going wrong with your configuration...
I have exactly the same problem
I have CS6 Mastercollection with educational license installed on both my laptop and PC
however they are not mac they are WIN7.
however my laptop doesn't have this issue but my pc does.
would this solution work for windows too? if I just grab the file from my laptop to my pc?
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 firstname.lastname@example.org since its difficult to view it on a forum.