http://blockchain.info/tx/52a875a46d7973760974b2ae8fa7bb71bfe7d06e0be8fd2bf2e20eaca182dbd7
When I enter the purchasing address (196V2uB471HoMHwbkQRQRiwd3aYpU6RtWg), I get "Bought 210000.0 Mastercoins and got a 88206.42361111111 Mastercoins extra."
The buyer sent 420 BTC with 5 inputs of 100 BTC each and 80 BTC change, which should have been 42000 MasterCoins plus a bonus. 42000*5 = 210000 which implies each input is being counted.
Probably related is the bug in the handling of this purchase: http://blockchain.info/tx/37992e445c33dd74a1e4e00dabb6a66f16a5d39977a1f5fd1a6c0154e884eee2
15XJoDF4xCUrWX3ES9ftWq3wnGhuRsqrLk (which had the largest total input) should be the owner of those MasterCoins rather than 1G6F8aMJNp3zMG9L1DxDT3WjiUntJYwYka (which had the largest single input). MasterCoin-Explorer incorrectly credits the latter address with the purchase. I realize I need to be more clear in the spec about how to do this!
I've fixed this individual issue. But I'm going to run through all the transaction this weekend to make sure I got all edge cases.
It looks like first part is fixed, but the last part (15XJoDF4xCUrWX3ES9ftWq3wnGhuRsqrLk vs 1G6F8aMJNp3zMG9L1DxDT3WjiUntJYwYka) still remains.
Very few purchases are affected by this (hopefully last) bug, so I went ahead and put a link to MasterCoin-Explorer.com in the OP