When you put the different releases of the software on, did you use the empeg upgrade utility, or did you flash the kernel in directly? The upgrade utility would reload your non-music file systems completely, restoring the config.ini and everything else to factory default. It might be a good thing to try if you have not already used it. If you have, that eliminates the config.ini and software load.
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Paul Grzelak
200GB with 48MB RAM, Illuminated Buttons and Digital Outputs