On the other hand, I occasionally see shares that are clearly within a block, have valid merkles and nonces, have a valid hash, and are not duplicates, but that nevertheless get rejected by the target pool, even as many other shares of similar age get accepted around the same time. Why does this happen? Couldn't really tell without knowing the internal workings of the other pools.
It would be very interesting to see statistics about that happening: which pools are affected and how many percent of valid shares are rejected?
I noticed differences in stale-share percentage while trying all those pools but my hashing-power is rather low and the timeframe was too short to get statistically significance.