I just processed my second flight where I deployed two cameras. Canon D10 is shooting 6.2mm (28mm at 35mm equivalent) and a canon EOS M shooting at 40mm. There's a screenshot of the broken alignment attached.
I also upgraded to build 1847 just to compound the confusion. Loaded camera models for both cameras from my previous successful surface model construction and got an interesting result - the whole model aligned, but there is a break in the ground plane and the terrain shoots off into the sky at about a 30° angle.
I would understand this better if there was an overlap issue with my 28mm photos, but the plane flies at a constant elevation above ground and gives me a good (about 80%) along-track overlap, and the flight lines give me about 70% sidelap. So the only thing I can figure is that the addition of the 40mm photos (0 overlap, random sidelap) screwed up the surface reconstruction. Although it worked fine last time. I'll test this theory tonight, but I've done about 40 flights on this same area, and haven't had this happen before, so it seems like it's either the additional camera or the latest build.
I think I can probably fix it by adding all of the GCPs but that will probably be a pain with the offset terrain. I think it will probably also fix if I re-run the alignment without the EOS M imagery, but I don't know a way to then run a second alignment to only add the EOS M imagery. I am wondering if it might also make a difference in which order I load the images into the project. Looking for any advice.
Also just FYI, My goal w/ the 40mm imagery is twofold. First I am testing the camera to try to get it taking pictures reliably and rapidly so I can replace the 28mm with it. Right now I can only maintain focus if I stay in autofocus mode because the temp change from the ground apparently messes w the pre-focus to infinity. Unfortunately with autofocus it only takes pics about every 5 seconds which is too slow. Second purpose is to increase ground resolution. Even though I don't have good overlap, that's provided by the D10, and the EOS M effectively covers about 80-90% of the survey area (based on my guesses from registering about 150 GCPs on every image). It worked great on the last flight, but This one seems to be an issue.