Hello dalnurse,
Unfortunately this could happen.
The point is that the file could be created with one muxer and AVI Trimmer + MKV use another one.
But to make sure that this is not a bug, please send us your file for we could check it.
You can upload it to any file host service, e.g. to
dropbox.com.
And please specify start and stop time positions were chosen for your fragment.