Media Encoder Stops Encoding with the New CS5.5

I just upgraded to CS5.5 a yesterday and having some issues encoding an 1 1/2 program for a DVD. The program doesn't seem to crash per se, just stops encoding. The task manager says it's running. I tried to encode the same sequence, but shorter and have the in and out points go through the part where it always stops and it worked fine. It's just when I try the entire sequence it stops. Anyone have any experience like this with CS5.5 just coming out?
Thank you,
Doug

Well, my problem happened with CS5, not 5.5. I don't encode enough to be able to say that it continues to be a problem. However, I would still pull up my CS4 AME if I needed to encode something again. But honestly, it sounds like the same problem as I had. My problem may have been further complicated by running CS5 as 64 bit.
For the record, I was never able to fully encode the f4v file I was given. AME behaved as though it was corrupt at the same point each time, shaving off about a half hour of the presentation. For several days I thought it was only a half hour presentation! I was given this file by an a/v company that caters corporate meetings. It was a video that combined a Powerpoint presentation and the audio from the podium. I asked for a file that I could use for Flash because their world is all Quicktime.
As I said, in the end the only way I could salvage this project was to extract the audio by encoding the f4v with Quicktime Pro and then use a third party software to marry it to the PPT presentation for a flash movie. That is a whole other issue I wish Adobe would look into, being able to encode PPT for flash. Corporations are doing some really cool presentations for business but MS just doesn't play well with Adobe Flash. It would really help me to be able to take my client's stuff and put it up on the web easily.
The young guy I work with said it was the lack of Quicktime codecs on my computer that was the hangup because in all likelihood they encoded the f4v with Final Cut Pro.
I work in a broadcast HD tv station. We are attempting to transition our clients commercial material to database for use on-air using computer files they provide (to get away from video tape). I can't tell you how much trouble missing codecs has been with this. Clients make their stuff in all kinds of environments and it can be professional or amateur. Sometimes the video is there but the audio is missing or vice versa. Sometimes one 30 sec spot will be fine, but the next one in the same file will take a 30 sec spot and stretch it into a 5 min timeline, losing the audio and playing the video slo mo. Our editing system is Grass Valley's Edius so that adds a whole new problem with codecs. It took us a long time just to figure out how to open a .mov on a timeline. So in the end we replaced one headache with muliple tape formats to a bigger headache with multiple codecs and proprietary software programs.

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