I have a main Desktop and a laptop both running Linux Mint 16. The Desktop is the host machine with 2 screens and the laptop is slave.
In normal Linux programs I have no problems at all.
But if trying to interact with windows programs under wine I have problems. I am an eve online player and usually multibox with clients on the Desktop and on the laptop. I've found that after activating synergy on the host if I move focus to the laptop and move back to the desktop, left mouse clicks are not registering correctly. I usually have to click on items twice to select them and there is no mouseover functionality until I stop the synergy server and all is well.
When synergy is running the first click acts like a mouse over, the second click acts like the select. The issue presents it's self more prominently when I right click to get a context menu. There are no problems with right clicking and the menu appears straight away. When I left click on an option the menu closes.
To get around this I have to constantly right click the blue/green icon in the menu bar and stop the server when on host and start if I need to do anything on the laptop (slave) clients.
This behaviour is only on the Host (server). Everything on the slave works fine.