I observed similar behavior on 2 different seedboxes with rTorrent + rutorrent.
When i add 4-5 torrents with plenty of seeders - the download speed goes sky high and then:
- On one seedbox rtorrent just crashes and I had to restart it manually through SSH.
- On another seedbox it shows 100% on all downloads and then XMLRPC error and then the whole download process restarts from zero at much slower pace.

On first seedbox i was able to manually clean-rebuild + reinstall rtorrent and then it behavior greatly improved.

I tried transmission on both - and it heaves in much more stable and predictable fashion. The only thing against transmission is that it's web interface is very functionally limited (you can only add/remove torrents and see basic stats).

I'll be trying deluge sometime...