Done all of that.
The problem is with Transmission's scrape and announce.
Looking in the Tracker tab (a useful addition which has proven very revealing with this issue), the time to announce and time to scrape count down. As soon as any of the timers get down to zero, all torrents drop off to zero k/sec. Approximately 60 seconds later, transfers come back and resume until a timer in any torrent gets down to zero. This occurs regardless of whether the torrent is paused or running/waiting (scrape/announce occurs for paused torrents), which means that the fewer torrents you queue, the better your chances, since it is entirely conceivable that you will end up in scrape/announce hell with timers hitting zero every few minutes or so. The issue can also be immediately triggered by choosing "Update Tracker" from the Transfers menu (if it is available).
During the times of normal activity, Transmission performs like a champ. I'm on 512/128 and was getting 50KB/sec. But with an interruption every now and then during scrape/announce. Other applications on my computer are not affected. Indeed to the contrary; when a scrape/announce occurs, my browser suddenly becomes very speedy as torrent speeds plummet, until 60 seconds(ish) later when normal Transmission activity resumes.
My observation is that it is most prevalent, and exceedingly replicatable, with torrents tracked by PirateBay trackers, such as open.tracker.thepiratebay.org (eg: eztv), to the point where, if possible, I will choose a torrent NOT tracked by thepiratebay.org over one that IS. With torrents off other trackers, such as some private ones, in many cases I have not had an issue. Certainly this suggests that something funny is going on with these trackers (being slow to respond or something), but Transmission is handling it badly, since this does not seem to affect other clients such as Azureus.
With such torrents, it is not unusual to have to wait 5 minutes before starting to get any kind of transfers happening, as Transmission announces, hangs, scrapes, hangs... even longer if it needs to fall over to another tracker (again, eg: eztv torrents often list 5-6 trackers).
