Right now I have my left monitor in portrait position and my right monitor in landscape.

If I have sourcetree on the right monitor and open Tools > Options the resulting window is extremely tall and extends beyond the top and bottom of the screen making it impossible to either move the window or press [ok]

My guess is that it sizes the option window according to the 1st monitor instead of the current monitor.

Currently an issue in 2.1.2.4

This is one of many many issues introduced in 2.x, Please do better testing before releasing new versions, it seems with each update that 1 bug is fixed and 5 more are added. For the last few years I have been using source tree it has been going consistently downhill