Add the line
IgnoreWrapAroundFragmentation(yes)
to your Settings.MyD file. If a file is fragmented, it will be displayed as fragmented.
The setting was introduced in 4.1.2.
When I do this in 4.3.1, the file still shows in yellow as fragmented, the status bar text lists "Fragments = 2".
Is there a way to color just these wrapped around files - separately from the rest of the "truly" fragmented ones?