Let me clarify: the position where application windows are disaplayed doesn’t depend on the NoMachine software, but it is possible that, if NoMachine resizes the remote physical desktop to a lower resolution than the one you use when being physically in front of it, some of the applications remember the previous position and are moved off screen after the resize (this anyway looks like a bug in the window manager that should prevent that). Assuming this is the case, you can try to choose a larger resolution for the remote dekstop (you can find a Resolution slider in the session menu panel), if available.
Does the paid version use a different way of connecting?
NoMachine products from the Terminal Server family (from Workstation on) allows to create multiple virtual desktops, that are independent from the physical desktop of the server and have no constrain about possible resolutions (any screen size is possible). This also means that multiple users can use their own remote desktop independently.