>>Can anyone give some guidance on this issue?
Use Keil, it actually works.
Other than that, I presume they are using OpenOCD, you could perhaps check you've got current version, and command line or scripting into the debugger provides the right options for each of the boards.
I don't know if you're using two instances of the project/workspace, if not clone a second copy and see if you can convince it to behave properly.
