Well, finally found out what was causing the problem.
Lenovo includes with their Laptops a program called 'Lenovo Auto-Scroll Utility'. This is referenced here: http://download.lenovo.com/ibmdl/pub...s/81vu22ww.txt
This program provides a function to improve usability for window operation.
Window position of the foreground application is automatically adjusted.
Well, there is a glitch with this program. The glitch is, that it ignores certain scenarios, such as dual monitor setups, where one monitor is set at 1920x1080 and another at 1280x800 (Which was the case for my user having a single monitor and laptop display). As described earlier, if you put the two displays, so you basically have a 'screen' of 3200x1080 (Side by side), there is a dead space of 1280x200.
Under normal circumstances, there is no issue, HOWEVER, when you go to a Terminal Server with 'Use all my monitors' checked, the Utility kicks in, treating the screen as being more than it should be and scrolling or panning things based on that orientation. Which also includes if you try to go into the 'dead' space on the laptop screen, it tries to go into that dead space on the laptop and moving the desktop from the Terminal Service downward, causing serious confusion for users.
Turning this Utility off, stops the issue. I didn't know this was causing the problem until I noticed the process running on another computer.