Are you using the 'q' action to override the order of what's being played (per the items with duplicate numbers noted against them) or just double-clicking on the duplicate item & then modifying the playlist? Also can you confirm what WACUP version & build type is being used.
Build is 1.99.43.23234 (32bit)
I'm sorry but I don't fully understand your question but I try to explain my workflow to reproduce the bug:
I've got a playlist. Now I drag and drop another song from the media library to play after the currently played song. If the currently played song is already in the playlist at an earlier position, the first occurance is marked as "now playing"
You can try it out quite easily:
1. Use an empty playlist.
2. Add the same song twice
3. Play the second song
4. Enqueue another song
5. The active song is now the first song