The issue is, when you move a window using the titlebar, fluxbox uses the pointer coordinates from the motion event, which may not be the same as the button down event if the mouse was being moved. The effect of this is that sometimes the pointer would appear to be dragging the window from some other point which may not even be on the window. It's kind of an unsettling effect that has been a 'feature' of fluxbox for a long, long time.
The solution is to use the coordinates of the last button press event when fluxbox starts moving the windows from the titlebar.
Note: Fluxbox already does the right thing when moving windows when not using the titlebar (i.e. the event manager, alt-click and move, etc).
To apply the attached patch:
git apply 0001-pointer-...-bugfix.patch
Developers, please review the patch for possible inclusion into core.