Hello Broken Arm,
Do you have all images in the same camera calibration group in Tools Menu -> Camera Calibration dialog?
Which camera accuracy settings you are using and which optimization options you are using?
I could assume that there are almost no valid tie points between the images from the separate flights, which could be a result of different weather/light conditions or changes in the actual scene.
What I can recommend is to split the calibration groups, just for case, in the Camera calibration dialog according to each flight (at least one group per different day) and re-align the set, if you see that there is bug number of invalid tie points for the image pairs from the different flights.