Sorry LJ, I don't really know, but this is how I personally think of it...
I think your subconscious mind is only trying to help you. It sends you thoughts it thinks you want. But it's not very good at it! When it sends you intrusive thoughts and you react by being frustrated, anxious, and unhappy it thinks... 'Hmm that thought I sent provoked a big emotional reaction - so it's obviously a very important thought for him - so I'll keep sending it. Yes, that should help!'
I think that's why they say you shouldn't react to intrusive thoughts. Then your subconscious will think you don't need that particular thought and after sending it a couple more times just to check it'll then try sending you a different thought. Unfortunately, that's often another unpleasant thought!
So you may need to stay calm and stay emotionally un-involved to several unpleasant thoughts in succession (much easier said than done) until eventually your subconscious will decide 'he doesn't want unpleasant thoughts today so I'll send him something nice!'