I figure someone have done this before but I post it again so new person can learn:
- set up TMPEnc w/ your settings
- go to setting-advanced and select the source
range to pick your start frame and end frame
- save the project
- repeat these for next MPEG files (with different
start and end frame, of course)
- finally, load all the projects and do batch encode

I think this is better and faster than encoding the whole AVI and cut it later. I also had a problem of using TMPEnc cut, the file becomes 2.0 non-compliance under Nero after cut.

Hope this is worked for you...