After another month of back and forth with Adobe tech support, this issue remains unresolved. Projects using MPEG2 or any other royalty-bearing codec are completely incompatible with Adobe Premiere CC installed using the Creative Cloud Packager (e.g. Enterprise Edition).
We were using the CC serial number that was shown for our university but that one does not include the codecs. The serial that should be used was under the larger organization of schools in the Adobe Licensing Portal, but by default that is only shown to the primary account contact (which is not me). I was able to use the Adobe Provisioning Toolkit to reserialize our installs with the other serial, which licensed the codecs and resolved the problem.
Erik is correct. There are two serial numbers for Enterprise editions. One is for a standard installation, the other is for the royalty bearing video codecs. If you are using any of the video applications, you need the serial number for the royalty bearing video codecs. If you use the wrong serial number, you will not have access to MPEG2 codecs. See your IT manager, or the equivalent to resolved this issue. 1e1e36bf2d