If you are using a left-handed mouse with Synergy cross platforming your linux and windows box, and if the windows box is the server, you just need to reset the linux mouse setting to right handed and change the windows mouse setting only to left handed. if you have both them left-handed, your linux will become a right handed mouse. I am not sure, if it is windows that is not sending mouse orientation information, synergy or linux, but it seems like, making a left-handed mouse in linux, will exchange the right and left mouse buttons with each other. If it is sent to be a left-handed mouse (let’s say from a windows box), then it will reverse the buttons in Linux resulting in a right handed mouse for you on your Linux box. However, if you are using Linux as your Synergy Server, it won’t have any problems such. This is the solution I do suggest, to use Linux as your main box, why I am not having my own prescription? The only reason I used windows as a Synergy Server is because I have Linux installed on my laptop and don’t want every time to attach and detach my mouse and keyboard to it.
Have you ever tried to change your mouse orientation from right to left handed ? If you haven’t done it, do it right now, it is challenging not only for your brain, but also for your hand :-).