If you receive coins via two or more addresses in the same wallet, where the coins originate from the same sendmany transaction, the sum total of the coins will be attributed to the first receiving address and the others won't show up.

To reproduce:

1. Set up testnet in a box
2. Start bitcoin-qt pointing at datadir 1 (instance 1)
3. Start bitcoin-qt pointing at datadir 2 (instance 2)
4. In instance 2, create 2 new receiving addresses labeled Address A and Address B
5. In instance 1, create a new transaction sending 1 BTC to Address A. Click "Add Recipient" and add a second payment sending 2 BTC to Address B. Send the payment.
6. In instance 2, it will display that you received 3 BTC via Address A, and Address B will not show up anywhere.