To recreate:
1 Open a Transmission standard window and open the inspector.
2 Open another app in a different Space than Transmission and give the new app it focus.
3 Switch to Transmission by clicking on the Dock icon or Cmd+Tab.
Focus will always switch to the inspector. Using the Dock icon, the regular Transmission window never gets focus. However, if you click enough times, it will switch to the regular window and the Space holding it. Usually 4 clicks, but it varies. Using Cmd+Tab is less predictable.
Using Cmd+Tab with the cursor (hold Cmd, press Tab once, then use the cursor while never letting go of Cmd) and continuing to click on Transmission, even when the inspector has focus, reveals some bizarre behavior. I haven't figured out the pattern yet.
Transmission 1.71 (and previous versions)
OS X 5.7