aimersoft mkv conversion problem...

[freewheelin]

I am trying to covert some mkv files to mpg2 using aimersoft Total.
The first two sailed through and I was impressed with the results, but subsequent files do not work. When I start them running, the "Elapsed" time does not correspond to the "Converted length of current file" time.
The conversion stops after 18 - 27 minutes of conversion, although the "...current file" time has raced ahead to the time of the full file.
I could then crop and convert the rest of the film seperately, but as this software has worked on some of the files, I am wondering why it will not do the others.
Any ideas?

[freewheelin]

A bit more info:
The two times run at the same speed for a minute and a half before the "...current file" time speeds ahead...