I have just added an extra PC to my Synergy setup, and found that it was confusing some keyboard characters. Particularly it was translating an entered @ to a capital Omega. After a bit of digging, I found the following discussion:
The eventual recommendation is the following fix. I tried it on both an Ubuntu Heron system and an older Fedora 5 box, bot are working much better now.
xmodmap -e "keycode 53 = x X greater greater greater greater"
xmodmap -e "keycode 52 = z Z less less less less"
xmodmap -e "keycode 24 = q Q at at at at"