The problem is that by default FileLocator Pro treats MSG files as being in the Outlook MSG format. There are two related settings that can help:
1. Remove the association between .msg extension and the Outlook MSG format
To stop FileLocator Pro performing any special processing on MSG files simply delete the msg entry in the Configuration->Extensions->MSG Settings
However, this has the side effect of preventing FileLocator Pro searching MSG files that ARE in the Outlook MSG format.
2. Instruct FileLocator Pro to always search MSG files
By default the setting Exclude file type from content searches when not active is set for the MSG Settings. This stops FileLocator Pro searching MSG files if the MSG extension has not been switched on in the Options tab.
Uncheck this option to allow FileLocator Pro to always search MSG files.