If you stop playback, then you also stop Play Doctor. The tracks already loaded into playing now will remain, but resuming playback will play only those tracks, without any Play Doctor magic. Could that be what you are experiencing?
If you skip a track,
while it is less than 50% played, Play Doctor will modify the playlist excluding tracks it sees as similar to that that you just skipped.
If you let it play, skipping tracks you don't approve of, it should add tracks ad-infinitum, until you press Stop, so, there should always be 100 unplayed tracks in the list. In my experience, I only need to skip at most four tracks near the start of my Play Doctor sessions, and the rest of them are then on the money. I'm a big fan of Play Doctor. It's very good at what it does.
...as I configured quite a few filters.
I think a good tip is to keep the filters as general as possible. This gives Play Doctor as much scope as possible to work with. For example, my stock Play Doctor filters are:
[Media Type]="audio" -[Filename]="//" [Last Played]=>7d -p=hidden,recycle [Rating]=>=3
So, only audio, nothing with a forward slash in the filename (excludes online streams imported to the library), nothing played in the last seven days, nothing on my 'hidden' or 'recycle' playlists, and finally, nothing rated less than three stars.
Within but a few skips at the beginning, Play Doctor has worked out what mood I'm in and delivers a really good playlist.
Are you running Play Doctor from your desktop in standard view?
If yes...
I set up a global keyboard shortcut (Ctrl+Alt+R) that kicks off Play Doctor regardless of whether or not MC has focus. It has worked well for me for a number of years now. If that's something that interests you, let us know and I'll show you how.
-marko.