I too have had this problem for months now but I have only recently brought it up to Symantec. The patch compliance reports for Adobe Flash Player bulletins are inaccurate for me.
I have over 3000 Windows XP systems to which I deploy patches but only 377 show up as needing the APSB13-05 bulletin. I have had to use a custom inventory to collect version data for installations of Adobe Flash Player instead of using the built-in reporting that is not working properly.
I have no problems with MS patch compliance reports or even with Shockwave or Acrobat. Only Flash Player is not reporting the correct number of applicable/installed/not installed.
Hopefully we can find and share a solution.
Thanks