As Letum said, you have to set the dimensions of your trackclip in the freetrack software
In my case, I removed the IR filter and it didn´t affect the image that much, so it can still be used for video calls. I would recommend that you first try to adjust the camera without removing the filter and in case you don´t get good results then remove it.
In this links you can find some tips regarding the camera configuration:
http://www.free-track.net/english/hardware/webcam.php
http://www.free-track.net/forum/index.php?showtopic=455
One trick I use to increase the size of the dots is to defocus the camera.
Hope this helps.