When the Access Fault box pops up in the debugger are you clicking OK and hitting the "play" button in that window above it? That will allow the boot to continue to the next fault. It's worth reading the debugger section in the how to install D11E4 document. You can also tell the debugger to not stop at certain faults so it won't "bug" you as much. I don't know anything about debugging, I just hit random things whenever there was a fault and it usually moved a little further. You can get the debugger manual here.

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Thanks - I gave it another try just now with your instructions but as soon as the Access Fault message appears I click OK and then the mouse cursor changes to a symbol with two arrows pointing towards each other and the debugger appears frozen so I can't click on the button that you mention, then after a while it says that the connection with the "nub" has been lost due to a communications error (too many retries) and that I should re-execute the target application

I'm starting the debugger application, then starting up the 6100, it just sits there until the "Welcome to NuKernel" appears and then it says "Getting process information" and it shows the kernel as being executed, the error seeming to be in that as it then changes to "Stopped" afterwards - does it sound like I'm going about it in the right way? I tried unticking "Set stop for Debugger()/DebugStr() default" and "Stop on code loads for existing processes" in the "General Preferences" section of the debugger.