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Which brings me to bug number two, the major one: the upgrader no longer works when Alpha 11 is already on the Empeg. It always times out now. using Emplode 2.0 or 2.1 makes no difference. Once you have an Alpha 11 on, you have it for life apparently. I tried changing the timing of when I start the upgrade process but it doesn't seem to matter.

Don't see how that can ever happen. The bootloader is protected (unless you've linked the two pads inside) and that allows you to replace the kernel which allows you to write to the HDs.