That is exactly what it is designed to do, so it shold work ok for you. There was a pach released, make sure it is current.
What HW/OS are you running? What type of files are you encoding and to what?
XP Pro (x86) SP3
Quad Core (Q6600)
Nvidia GeForce 8600 GT
I installed the 4.02 update for Media Encoder, but before it was doing the same thing.
Sometimes it would work, sometimes it wouldn't.
I was trying to encode wmv files to avi.
It could be there is something else running that is causing this, but I tried closing basically everthing else, and still not stable...
4.02 is stable for me so perhaps it is what you are encoding. I have never tried wmv to AVI; i typically go from the timeline to web formats. Do the other adobe apps seem stable? Is it just AME? Im not sure elese to suggest other than a clean install.