This drives me a bit batty and I'd love to see it fixed.
Say I have two plugins on each channel, an EQ and a compressor, the compressor is pinned so it stays open when I switch between the plugins using the Edit Plugin select mode on the Faderport. When working on the first channel I have both plugins opened and laid out side by side.
Now I hide my plugin windows and select the next track, I open the pinned compressor and it appears in its original position, but then I open the EQ and it appears in the same position as the compressor, instead of where I last moved it to (eg to the left of the compressor).
If I remember to do it the other way round, it actually works. If I open the unpinned EQ first and then the pinned compressor, then they generally open in the right spots, but I'm constantly ending up with unpinned plugin windows forgetting where they were before and opening on top of some pinned VST.
Perhaps if I just pin everything it might work better - but I'd love it if there were some better management options for this behaviour.