About the calibration problem:
I am pretty (100%) sure that your problem is caused by incorrect led installation. If you have problems with the bottom calibration point, the camera doesn´t see the single led on the right properly. The leds MUST point towards the camera (as described on the Ultimarc website) and if you have installed them in a bezel I would recommend a minimum of 2.5 mm (1/10 inch) of the leds sticking out.
About the red dot:
The red dots moves in the opposite direction because the sensor view show what the camera sees.

This is the way it is supposed to be.
The aimtrak is a very good (most probably the best) gun system for the PC right now so I hope you get them working right.