Hello Janbert,
Can you send a small subset of images (just for a few camera locations) to support@agisoft.com, so that we can reproduce the issue?
Also please specify, if you are using Reflectance Calibration operation in 1.4.5; whether you have tried to switch the primary channel to NIR and adjust the brightness and if during the export you are using any Raster Transformation option (like Index Color) - since the source data is four-band 16 bit data, and in the output, according to your description, you have 8-bit RGB + alpha channels.