I found this thread by Googling, I had a very similar problem to your first question.
It reminded me of my problems with utorrent years ago where it would lock up whenever I added a new torrent. Turns out that pre-allocate all files was turned on and when I would add a new large torrent it would lock up for however long to took to write out the allocation.
Taking a look at the advanced options I didn't see anything relating to file allocation but Disk queue size: 1024 kb did catch my eye.
That seemed very small considering that I have 32GB of RAM so I upped it to 102400kb and restarted the torrents.
It's been working now for several hours at several MB/s whereas before it would slow right down to 50 KB/s after 15-20 minutes.
I would try adding a larger disk queue size to see if it helps with your issue too.