This is just a GUI display issue. A 40 MHz channel is actually two 20 MHz channels mated together. The control channel is the lower 20 MHz. So while the AP displays the "center" of the 40 MHz channel, the SM displays the center of the lower 20 MHz which is the control channel. We will fix this display issue in the next release to avoid confusion.
As for the throughput, it is not related to the mismatched display in channels. What kind of throughput are you seeing? What do the Wireless Link Test results show you? Have you made sure the 40 MHz channel you are using doesnt have too much interference by running a Spectrum Analysis? Also have you made sure of the best alignment possible (Tools->eAlign can aid with alignment).