My rejects are through the roof... I have discovered 1000s of blocks for WafflePool, of which only a few were orphans.
What made WafflePool seem so fair previously, IMO, was that share generation was statistically consistent between mining fast coins and slow coins. Now, a share is "worth more" then a slow coin share, because the slow coin will have less shares lost to 'rejects'.
What is "through the roof"? Share value shouldn't change, as slow/fast coins are spread amongst servers evenly, so you'll have some sections of time where you mine fast coins (and get a slightly higher reject rate - I'm seeing 5% avg rejects on fast coins), and times where you'll mine slower coins (seeing 1-2% reject rate on lite/doge). But those will even out to be the same for all miners.