There are a few possibilities which might be the reason for your issue:
1. The line/phase separator in the stencil you are using has been redesigned (if you have updated Visio since it was previously working). If you had an old Visio file with a separator that worked the way you remember, can you paste it into the new doc to see the old behaviour or does it not work in the new doc?
2. The separator may have a setting which relies on a Document or Page setting for its behaviour. If you do a detailed review of the shapesheet fields for that separator you may discover a clue there.
3. This is a longshot but perhaps it is possible for the swimlanes to be on different layers which 'could' impact the separator. I assume that the swimlanes have to be on the same layer to actually work but it could be a possibility.

If you could post sample doc(s) which show the separator working/not working then it would be possible for me to examine your docs to see if there is a logical reason for the changed behaviour. I don't often do swimlanes diagrams and would need to play with one of your sample docs to see how your shapes work.

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Andrew Lockton
Chrysalis Design, Melbourne Australia