Audition CS6 Multitrack - clip in/out points arbitrarily changing

Using CS6 on Win7 64bit in multitrack mode.
Assembling music and voice clips on the timeline to make a programme, saving as I go, and working usually from start to finish, CS6 is truncating some clips after assembly and saving, leaving gaps in the sequence, meaning I have to re-edit and resave.
Clips can have ends or beginning truncated, and it happens on music and voice clips, arbitrary timing of removed sections.  I can reopen a saved project to find new gaps in work I had already completed.
Thoughts?
Christopher

The project comprises music tracks, either mp3 (or variants) or wav, copied into a project folder on an external drive.  A project is started at home on CS6 usually by my wife just assembling the music tracks in play sequence on the timeline, leaving gaps for voice tracks to be recorded in the studio at our local hospital radio. I only get involved with technical issues, and it is a technique she has used many times.
In the studio we load the project from the external drive into CS6 on the studio pc, and record her links on a spare track, at the approximate location on the timeline where it will be used in the final programme.  Each link is recorded separately so Audition gives it a unique filename.
At home it is just a question of her assembling the music and links, editing each voice track if necessary for restarts, then dropping it in place with fades etc as needed. Usually all that is needed is to trim the voice track start and end to remove unwanted lipsmacks or dead air etc, which she does by dragging the clip ends.
It's a technique that is quick and easy, but lately she has complained that her Audition is arbitrarily chopping chunks off the beginning and end of clips on the timeline, including the music clips, leaving gaps on the timeline.
I've just loaded up the project from the external drive into my install of CS6 (both hers and mine are legit, and not the same serial), re-edited part of the project and saved it.  When she reopened it on her pc all my edits had disappeared.  The same happens if I now open it on my pc.
I've been using Soundbooth/Audition/Premiere pro for a decade or more so it isn't finger trouble, something odd is occurring!
Christopher

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