I found that going into Media Cache Files and deleting ONLY the files associated by name with the clips that are in trouble solves this problem. I notice multiple attempts to create these files (likely corresponding with the repeated unsuccessful attempts to conform), often with a _1 extension on the problem files. Completely deleting these files on three clips (out of about 12, 9 of which were fine) that were troubled caused them to conform one last time, and conform properly.
Before taking this step I observed a clip audio track that suddenly cut out completely at about half; listening to it showed that it was troubled (in-and-out, sync and other problems) even before it cut out completely. The audio from my .m2ts files (created by a Sony HDR CS-550V), played in VLC Player perfectly.
The files, on a PC, are usually located at c:usersappdataroamingadobecommonMedia Cache Files. If you don’t see an appdata folder under your user name, you need to open a Windows Explorer window, press to activate the menus, choose Tools Folder options, press the View tab and choose Show hidden files, folders and drives.
I don’t use the program on a Mac but believe that the same files are stored there.
Jay from the Bronx