I can't offer you much help, although I can see no reason why it shouldn't work if you can somehow tell it a different device ID and core IP.
The core will generate an Orbiter interface for a particular device ID that will only work with that Core, so if you do that on each core then as long as you can tell it the Core IP (Which you can) and the device ID (which is the bit I can't remember) then there should be no reason why it shouldn't work.
Is this what you have tried?
On a side note, how have you set up your two cores? Different subnets using different hubs/switches? Is one of them still acting as a gateway? Is DHCP still running on both?
I assume you are running both as an evaluation to see which to proceed with, is this correct?
The web orbiter is definately an option, but it is a pain to use with the way it refreshes.
On another side note, the Windows XP orbiter works under Wine on Ubuntu 7.04. Although, it does seem a bit silly to be running a windows emulated version of what is a predominately linux product. But if anyone else has managed to just run a linux Orbiter then I would be keen to hear, I had no luck. (Note, the machine does not have linuxMCE installed, this is my everyday desktop at home)