OK I did find one outstanding issue with mastercoin-explorer - it still counts the same address multiple times in one purchase. For instance, on this transaction:
http://blockchain.info/tx/52a875a46d7973760974b2ae8fa7bb71bfe7d06e0be8fd2bf2e20eaca182dbd7When 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/37992e445c33dd74a1e4e00dabb6a66f16a5d39977a1f5fd1a6c0154e884eee215XJoDF4xCUrWX3ES9ftWq3wnGhuRsqrLk (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.