Remember that there are different types of conflicts. If a file conflict is red flagged (!), then you have location conflict where 2 or more apps are writing a file to the same location hence will step on each other. A yellow flag (?) on the other hand means that the file exists but in different location, so this is not necesarily a conflict, unless you have them writing to like System and System32, etc. Now if the files are being written to their program own folders, that is well and good.
Alternatively, everything could be peachy. I suggest you delete the app out of Software Manager and reimport the isolated app, then rerun conflict manager. Remember, we are dealing with a database here and spurios tuples can wreak havoc on the integrity of the reports you get.
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