There is a slight difference which I believe to be related to the delivery of the game, which is now HTML vs Java. In the Java version, once you started sweeping, it didn't matter where the mouse was in relation to other windows - Java still knew that you had clicked and continued to move the mouse. In the HTML version, however, it is the browser itself that receives the mouse input. If you "drift" off of the game window when sweeping, I think the browser loses track of the mouse and thus sweeping stops. The corollary to this is that the smaller you have the game window, the more likely you are to drift. Keeping the mouse in the game window SHOULD resolve you issue, I think.
Perhaps FoD can correct me if I'm totally off the mark on this one, but if I am right, I don't think there is anything that can be done to address it, given the way browsers work.