I was slightely confused by your question, since you didnt mention that you are using non-default settings.
Disable "Region Overlap" in "User Preferences - System"
If you want to use "Region Overlap" here is a small hackish patch to space_view3d_screencast_keys.py that should roughly do what you want:
scene = context.scene
mouse_size = scene.screencast_keys_mouse_size
tool = context.area.regions #coughs.. we just assume its there
w = 0
w = tool.width
pos_x = int( (context.region.width - mouse_size * MOUSE_RATIO) * \
scene.screencast_keys_pos_x / 100 + w)
pos_y = int( (context.region.height - mouse_size) *
scene.screencast_keys_pos_y / 100)
Whole file is here: space_view3d_screencast_keys.py
Just find your scripts/addons folder, move the old file and place this one there.
Slightly safer might be to query for the tools panel but it comes with some overhead:
w = 0
for region in context.area.regions:
if region.type == 'TOOLS' and bpy.context.user_preferences.system.use_region_overlap:
w = region.width