You can always send the faulty lenses in for repair. Sometimes the elements get out of alignment, etc. They should at least be able to test them out and let you know if they are within factory tolerances. Are they darker at every f-stop? Only around the edges (ie. vignetting?) (which usually shows up at wide open apertures...but that would normally not be a setting you would use for Photoscan, anyway)
Theoretically you could counteract the darkening in a tool like Lightroom, which also can correct for vignetting. I always use it to remove chromatic aberrations as well. If you know which lenses are darker, you could also change the exposure settings on those cameras to compensate. (ie. set exposure compensation to +1/2 stop, etc)
I've used Lightroom to balance exposures when there has been some variation, and it seems to work just fine. (make sure NOT to use ANY distortion correction, though!)