I just posted another update with a minor improvement (version 1.64) over the big upgrades posted a couple weeks ago. Specificically, I changed the "reprojection error" reported for 3-D points to reflect the root mean square difference, across all cameras, between the input screen positions of a 3-D point and the expected screen positions based on back-calculating from the measured 3-D position. The previously reported reprojection error was the root of the sum of these squared differences (instead of the mean square), which reflected the same information but did not have the same intuitive meaning.
The consequence of this change is that reported reprojection errors will all be a bit smaller than they were before. This doesn't mean the measurements got more accurate; it's just a better error estimate. And I would stress that both the reprojection error and the PLD error are not indicators of real measurement error (with which they are only loosely correlated). Instead, they are primarily diagnostics to help pinpoint major calibration issues or mis-clicks during measurement.
This change only automatically affects new measurements. Old measurements will show their previous reprojection errors unless you recalculate the calibration on one of the videos, which forces all points to be recalculated.