Compressor cutting out frames

Hello

Using Compressor 3.5.3. I'm converting H264 960x480 animation quicktimes to prores LT 1920x1080 both at 24 fps. For some reason on certain clips one frame is being cut out of each shot. All of my clips have counters on them so easy to see that the last frame is being clipped out by compressor. I made a custom setting for the project with the frame size and codec and then put it on current fps and the frame controller off, then I did a test to change the fps to 24 in the qt options and still clipped the last frame. Any ideas on what might be happening? Also I used mpeg stream clip and it made the qts correctly but wasn't preserving the aspect ratio that I need so I don't think I can use it to convert the clips any ideas?

Thanks,
Emily