1) Drag a clip into AE
2) Crop beginning of clip in comp by i.e. 200 frames
3) adjust inpoint work area
4) hit Adjust Comp to Workarea
5) save Project and open AME
6) Drag over the compostion to AME
7) render out the file
AME will NOT regard the NEW composition adjustments and thus render the 200 frames you cut off to the beginning of the movie...
Either I am doing something wrong (I hope but I don think so) or this is a BUUUUG...