BT.601 and BT.709 compatibility benchmark
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Regarding the flags, "Transfer characteristics" did not have an effect on any player. "Matrix coefficients" was the one that mattered in proper BT.601/BT.709 reproduction..."Color primaries" had an effect only on Quick Time...
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See also:
Color coefficients and Colormatrix usage summary
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every HDTV I have ever heard of uses Rec 709 primaries
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So my working rule is that as far as players are concerned, Matrix Coefficients matter, Primaries and Transfer Characteristics don't (except as noted above) - but set them all anyway when encoding, as required by the spec.
EDIT (to answer your question) I think the settings get mismatched when the encoder fails to explicitly set all three parameters, leaving those not set to either their previous or default values.