If it's not working then it probably has nothing to do with AMD vs Intel, and everything to do with either something in the game itself (for example they may be using some unexpected API that Inner Space is not correctly handling) or your ISBoxer conifiguration.
In your configuration I would ensure your Slots in your Character Set are assigned to different cores as you expect. (In the top left pane select your Character Set, then in the bottom left pane select each Slot number i.e. 1, 2, 3)
After checking that, I would open the Windows Task Manager with Ctrl+Shift+Esc, find the game clients, right click and select "Set Affinity...". The selected cores should match those configured in ISBoxer for each game instance; if not, then this would most likely be something in the game itself that I'd need to update Inner Space to handle.
Is it different behavior between AMD and Intel chip sets since Intel I7s and such use Hyper threading technology? If so what?
Intel's Hyper-threading is basically splitting a physical CPU core into two, and the CPU Strategy Wizard will then use 2 cores instead of 1 for a round-robin. The second core from each can't run a full game instance and we get better performance by making sure these are paired. So yes there is different behavior -- with HT (good Intel) you're setting it to use 2 cores and without (all AMD) you're setting it to use 1 core.
I haven't seen your configuration see if you've done something that broke it.
http://isboxer.com/wiki/Configuration_Sharing For example an easy way to make it not work is to create a Computer, change it to have "CPU Cores" set to 1, put the Character Set on it and then use the CPU Strategy Wizard (or just use the Quick Setup Wizard for that Computer). This would be easily recognized by checking the setting per Slot (as suggested above) though. Anyway, happy to take a peek.