I had the same problem - I'd imported a midi file then used the arranger to identify sections, finally selecting (in the arranger window) any sections I didn't need and deleting them. For my own convenience, I then moved all the remaining sections to make them consecutive and easier to work with.
I then modified these sections and created an updated arrangement from them, but the original end point still remained , so on playback, the file continued playing beyond my intended end (mixdowns were also the same.)
Here's a solution that worked for me -
Select the original end point using Ctrl-End
Drag out a new arranger section from 1 bar to the right of this endpoint back down to the section where you want playback to end
Using the arranger track (or arranger window) select this new section
Delete this new arranger section,
It seems that that the old endpoint is also deleted, so the file now stops playback the intended project end.
Hope this may be some help should you have a similar issue.
