We analyze a scenario in which software agents implemented as regret minimizing algorithms engage in a repeated auction on behalf of their users. We study first price and second price auctions, as well as their generalized versions (e.g., as those used for ad auctions). Using both theoretical analysis and simulations, we show that, surprisingly, in second price auctions the players have incentives to mis-report their true valuations to their own learning agents, while in the first price auction it is a dominant strategy for all players to truthfully report their valuations to their agents.