I can say SpyBot and AdAware haven't caused any problems at all for me. Though, looking at it, all my folders ARE read-only, it just doesn't encumber me since all it does is present me with an: "are you sure?" when I want to delete something and doesn't seem to interfere with any programs of mine.
I'm capable of downloading things, even of having programs download stuff for me, without any issues.
Perhaps your troubles originate from something other than the read-only folders?
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