Hi Kida. I didn't quite understand this sentence: "...the "forward"-action also becomes an "backward"-action... ". Did you perhaps assign Middle button both as a general gesture button, and as a button that is linked to a specific action? That shouldn't happen, since you can't press the middle button while holding down the same button - though I have no idea whether that would cause problems.
I also move files with the right mouse button all the time, and I also have the right mouse button as the gesture button. I set StrokeIt to have gestures "time out" after 250 miliseconds: this means that, if I hold down the right mouse button for longer than 250 miliseconds without moving it, StrokeIt lets go of the mouse, and you can drag files as you used to. When you let the button go up again, things are back to normal.
So if I want to draw a mouse gesture, I do it fast, without pausing; if I want to move a file, I right-drag the file to where I want it, then stop moving while holding down the right mouse button, then wait for the gesture's line to disappear, and let go of the button.
Have fun with StrokeIt!