Using Ubuntu 12.04 64-bit with Transmission version 2.51 (13280)
I am uploading screens for better understanding.
Transmission continues to Download the torrent even after Pausing .
Not just with particular torrent but all seems to do it. Seems to be occurring in file greater than 500 - 600 MBs .
This behaviour was present earlier version of Ubuntu too if my memory serves me right , but then ,due to Dual-boot nature i considered downloading large files in other Os.
At pausing ,
Downloading data, even after Paused.