I thought I would add my voice to this issue as well.
I deploy video on the web, and it has to be in all kinds of flavors..H264, Flash, WMV etc,
While the Media Encoder does a great job of encoding some of these files directly, especially the Windows Media Files, I need added functionality to the Flash versions, plus, It takes twice as long to encode these vs. Windows on encoder with virutally the settings. I know making a copy from a copy is dumb, but WME doesn't do all I need it to do, and takes longer to encode.
My workflow for several years has been to create a "Master" MPG2 file with as little compression as possible of the final video, I then copy it to a Mac to generate QT/H264 files and my editing computer encodes the Windows and Flash versions...halfing my encoding time.
I didnt notice any artifacts in the actual Master files, the Windows Media and Flash videos consistently create artifacts and "hiccups" in movement.
I remaster the master just incase something was wrong.
Edited another movie, same issue. Would consitstently artififact at a certain point or have movement stalls or hiccups in all sizes and in both Flash and Windows Media...so it just wasnt an issue with Windows Media Encoder...Flash conversion had issues at the same spots.
I really need these MPG2 files to be solid, because the Flash conversion utility I use builds skin player and builds the html that I use.
My worry was CS5 might be using the System Registry to track codecs and my CS4 would no longer make proper MPG2, specifically the MainConcept codec was damaged or new, but was pretty sure the codecs are built into Adobe's Encoder"
So my next step was to go back to CS4 and I edited a new movie, encoded my master MPG2 and then used WME to encode the three sizes of vidoe I need.
All are perfect with no artifacts!
I have opened both versions up and tried to find ANY setting that might be different that is creating an issue while creating the master MPG2, but all the settings appear to be virtually the same. There is a new option Render at Maximum Quality and have tried generating the master with and without this box checked (same for the the Render Maximum Depth).
Otherwise it all looks the same.
So I am backt to using CS4 until hopefully enough people will notice the issue with the MPG2 files. I think there is something buggy going on with the Encoder that might need to be tweaked.
I love all new updates to CS5---editing with color correction and full speed is awesome. But there is def something buggy with the Encoder on MPG2 files.