This post serves to highlight just how awkward my setup is, and as a guide to help with anyone with a similar setup (all 3 of you, worldwide).
I’ve recently started using Synergy to control my Macbook from my Ubuntu (10.04, if that turns out to matter!) desktop. However, I use the slim Apple USB keyboard on my Ubuntu desktop (a subject of previous posts here). They key mappings for Alt and Command on my Mac were reversed when I was controlling the Macbook. I.e. the Apple keyboard wasn’t being reported as such to the operating system. Here’s a snippet from the synergy configuration file showing the swap to make the Apple keyboard work as expected on a Mac Synergy client. If you use QuickSynergy, the config file is in
section: screens ubuntu-synserver: macbook-synclient: alt = super super = alt end