I just tried it out, and I cannot reproduce this behavior in 2.0 beta 12 (alpha team internal release only).
I did the following:
1) Created a "TEST" playlist with four tracks.
2) Created a "TEST WENDY FLAG". Assigned this flag to one of those four tracks.
3) Created a "TEST WENDY FILTER". In this filter, I marked it so that anything with "TEST WENDY FLAG" was preferred (i.e., a check mark rather than an x).
On the player when I select "Test Wendy Filter" from the Filters menu, it all appears to work as expected. The test track is the only one I see on the player. I am able to select and play the track in all of the ways possible: by searching, by navigating to the track, or by playing its parent "TEST" playlist.
Can anyone with Beta 11 see if they can reproduce the behavior? Perhaps it was a bug fixed after beta 11.
NOTE: Please check your playlist properties and see if you have any of the special flags checked such as "ignore as child" or "play X tracks at random".
ALSO: Anyone who knows about these things... is it possible for a deleted FID that used to be a wendy-flagged-Tune to get re-used as a Playlist, and then have the Wendy filters apply to the playlist (even though you can't change Wendys on a playlist)? Maybe that's the root of the bug?