It probably happens with some of the fast coins now.  I find the same thing occasionally - this is why I expressed a strong dislike for the rejected share scheme that came along with PW's new stratum implementation.

For a switching pool, what I used to like about wafflepool the most was that shares were shares, unless they were truly truly stale.  In my mind, it just decreases the appearance of variance, and eliminates the risk of coin penalty if the switcher is splitting hash between say litecoin and fluttercoin.