Hi Jeff,
I have just fixed the issue.
When starting Mach up and selecting the use the SS plugin rather than the PPort driver, I would then be confronted with a message saying that some of the SS settings were not set (pulse frequencies etc that you configure in the Plugin Control menu). There was an option to select to load some defaults (YES button) or load nothing and manually configure it in the aforementioned config dialog (NO button). I was clicking NO and manually configuring it. In the end I clicked yes and at that point the firmware was obviously flashed to the SS and the lights started flashing. Everything was ok then. The only problem is all of my settings have been wiped (ports and pins, motor tuning). Small price to pay though.