UPDATE FROM MABULA
I have had a very rough 2 months unfortunately health wise. I was struck 3x in a row with bacterial infections. The second infection occurred  after a routine hospital checkup and I became very sick. I had to rest and take a lot of antibiotics. Once I was recovering and restarting work 1 month ago, I again became sick. The infection was not yet gone, so even more antibiotics and rest was needed. Needless to say, it took a lot of my energy and I needed a lot of rest.
Finally, the infection is really gone and my energy is coming back step-by-step now and I have started work again. I am terribly sorry to have kept you waiting for support. I will address all outstanding questions and e-mails step-by step and will be on the forum daily from today.
APP 2.0.0-beta47 will come soon as well, a lot of work was already completed before I became very ill, so the release is also nearly ready for you. Beta47 will be much faster actually. Many workflows will be more than 2x faster, mosaics can even be 10x faster than before because registration really received a major boost... all compared to beta46. Â Before I release it, I will make sure that everything is working properly and then I will release it.
The images/frames of your DSLR camera are always crops of your entire sensor. All DSLR manufacturers make a crop of the entire sensor to present you with the image that you shot. So from each border, a couple of lines are removed in the raw converters.
This cropping is done at the end of the RAW conversion of the data. So the image dimensions of your calibration frames are the image dimensions of the entire sensor. That is the reason why you see this difference.
 What happens in calibration of a light frame, an example:
the light frame is reported as having image dimensions of 5184x3456, the calibration frames have the dimension of 5344x3516
- your light frames are read in the raw converter, this reads your entire sensor, so this raw image raster of your light frame is your entire sensor: 5344x3516
- this data is linear monochrome CFA data, undebayered.
- the calibration CFA frames are then used in the right order to calibrate the light frame. So your light frame raw raster data with dimensions 5344x3516 is calibrated with 5344x3516 calibration frames. So calibration is done on the entire sensor.
- After having applied all calibration frames, your data will automatically be debayered according to the settings in 0) RAW/FITS
- Finally, the fixed sensor crop is performed on your light frames. So from all 4 borders some data is removed. This leaves you with the 5184x3456 image dimensions for you light frames.
 So this means that you have a 100% guarantee that this is done perfectly, it will not cause trouble with dark subtraction or division by flat frames 
And that APP calibrates your data in the raw converter at the right moment. Other applications that use DCRAW (almost all other programs) simply can't do this.
