The Calypso markers seemed to work quite well for me. The only way I know that they really did something was in two sessions. One - I had some extreme back pain, and must have moved a tiny bit, at which point the calypso machine alarmed. In the other, it was gas, same thing but internal, the alarm hit, things stopped.
I do know that the surgeon put the markers in the prostate scar area, as it became more painful when he hit that mass. He did show me the overlay xrays of where the prostate was, and where the markers wound up. Also, they are not aiming directly at the markers. They are using them to create reference points for a 3-D map of the prostate bed area.
I had understood that the CT / Varian combo was to verify everything at startup of each session (the calypso monitors at the start, then all through the session - there is a panel placed over you that receives the gps-like signals, the CT may as well, but that was not described). This being from comments of one of the members who had that CT equipment 8 or 10 months ago - I had asked a radiologist friend (not one of my doctors) about that, and at the time, he said it was extreme cutting edge stuff, and there were just a couple of those systems in the field. He felt like the Calypso was a very valid choice as well.