I use Ameritrade quite a bit for my position trades, and I get partial fills on an almost daily basis.. I have never once been charged extra commission on the partial fill. If, however you get a partial fill on a limit order and you decide to take the remaining shares and sell them at a different price you will be charged as a new order since its considered a cancel/redo.
Actually- as much as people hate Ameritrade, I do about 5 trades a day on that account.. Every time I get a bad fill or other slippage/etc etc they make good and correct the error. Although to be honest- most of my trades are swing positions so the urgency and haggling over pennies isnt as important to me and that might explain my good experiences..
Brown and Co. is really really good as well..