It sounds like no matter what program you're using you'll need to do two seperate batch processes. One for each size. I don't know of a program that would seperate the pictures that you wanted into two seperate sizes and then process them.
I could be wrong though.
I only use 150x150 thumbs myself, but if I did two different sizes, I'd just do two batch processes. It only takes a few seconds per gallery.
I use superjpg and firehand by the way.
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