So I have an case open with Apple support on this, the support person was incredibly nice and attempted to help but he had to pass the issue onto 'engineering' & it appears they refuse to admit this is a major problem all he got back in terms of advice for me from them was to 'install firmware' for my external drives (never heard that in my life for a USB mass storage device). the other option was to completely reformat the drive and see if the problem returned.
Suffice to say no explicit drivers exist for my drive from the vendor, I did also reformat one of my drives (after having to move data off it), end result NADA, 10.8.2 solves nothing and setting the option for the drives not to sleep didn't solve a thing.
If anyone from Apple is listening, please stop trying to fob us off with bogus reasons why this is broken, my drives all worked fine on Lion & now I'm seeing issues on mulitple ML machines.
I suggest everyone raise this issue with Apple support, hopefully the volume may make them look seriously at this OS issue.