IRC user "CryptoSiD" reports that after restarting 0.10.1rc2, it displayed "conflicted" for two of the transactions he sent until he ran with -rescan (during which the transactions in question were mined). Specific txids, getinfo/getblockchaininfo, and debug.log are stored on my PC as "20150417-CryptoSiD-conflicted-issue" to respect the user's privacy - I can share these privately with other developers.
During the problem, getrawtransaction could not find the transactions. This suggests it was not in the mempool. User reports that he did not change versions or do anything abnormal between restarts or to send the transactions. I am unsure where we add wtx to the mempool at startup - assuming we do? Either way, we shouldn't report "conflicted" for a transaction just because it isn't in the mempool... even if we rejected it for some good reason (eg, different policies than when the tx was sent).