I am not sure if this was an intended development direction or a simple oversight. Up to 2.44 You could just doubleclick the active torrent file in transfers window to stop/start. In 2.45 this option seems to be either gone on purpose or is simply buggy.

Check your double click options in Settings -> Behaviour

For me its working, check settings -> User Interface -> Behavior -> Double-click Actions, maybe something wrong there. screenshot included.
http://puu.sh/roDbU/12505bea9b.png

There is indeed a problem with that setting upon upgrade, but it is easily fixed by going Settings > User Interface > Behavior > "Double-click actions" button.

Thanks for the solution, though it is still not certain is it a bug or intended behavior. For me start/stop is much better option for double click than Open Folder as it is set in 2.45.

Ahh I see. I already ran "Open folder", that's why I didn't notice any difference upon update.

There were some problems to settings listed in changelog.
Glad there's readily available option for you to check. :D