Microsoft Mouse and Keyboard Center App Specific button mappings

Potential Bug:
Open the Microsoft mouse and keyboard center, go to App Specific settings, add Starcraft II .exe and remap the left and right mouse buttons to be the opposite way around (say) to the desktop. For clarity, do the same with the Battle.net login exe as well. Close Microsoft Mouse and Keyboard Center. Then, observing which buttons are doing what, open Battle.net and interact with the interface using the mouse: use it to launch Starcraft II, and when this loads, again, navigate the menus etc using the mouse.

Behaviour (on my machine since the early June 6th update):
Battle.net GUI accepts/obeys the reassigned mouse buttons.
Starcraft II rejects/ignores the reassigned mouse buttons.

The above is of particular health concern for those who have already configured their desks as best as possible to prevent RSI, but attempt to reduce the risk of injury further by alternating handedness between rapid/heavy mousework tasks (like Starcraft II) and more mundane desktop tasks.

I’m seeing the exact same bug with Chrome; I found this thread while searching for solutions. The bug might be on the windows/microsoft side of things. The other option is that Starcraft II changed how it reads input from the OS in a way that bypasses whatever Mouse and Keyboard Center does.

Finally found something on the support site that might be relevant:

Note

If you open a program by using the Run as administrator command, you will not have access to application-specific mouse button settings. Instead, the mouse will use the global mouse button assignments. To enable application-specific mouse button settings, open the application without administrator credentials, or log on to Windows as an administrator.

support microsoft com/en-in/help/4052294/accessories-how-do-i-reassign-mouse-buttons

I can confirm that this was my problem. I have no idea how I had Chrome running as an administrator, but apparently I did. My only guess is that I happened to start the it via another program (i.e. from open-link-in-browser), and that other program was run-as-admin, and the setting carried over.
Your problem suggests that SC2 is run-as-admin but Battle.net is not. No idea why or how that would be the case.

My only suggestion is to reboot everything and carefully ensure that you do not accept any run-as-admin prompts, from anything. Hopefully you can run SC2 and it’ll be fixed. If it’s still broken, then your problem is likely something else. (It might be that you can’t get SC2 to run without admin credentials, in which case you’re hosed but at least you’ll know why.)