The images produced by Ekos are shifted 10 pixels in width en 5 pixel in height compared with Adobe Digital Photo Professional and ASTAP. This is not a major problem but doesn't allow the make darks outside Ekos.
For ASTAP (stacking) user, I have compared the hotpixels from FITS images taken with Ekos/Astroberry with CR2 darks and analysed them with Adobe Digital Photo Professional and ASTAP 1.0.0RC2. All images are in 5184 x3456 pixel format
These are the positions of two hotpixels:
CR2 dark using DPP (Adobe), positions 18, 314 and 152, 2802 (counting starts at zero)
CR2 dark using ASTAP, positions: 19, 3142 and 153, 2803
FITS light by INDI, positions: 29, 2147 and 163, 2808
So there is a shift of 10 in width and 5 in height between the INDI FITS and the CR2 dark. The fault lies in Ekos/INDI. For ASTAP the position of the .CR2 hot pixels are exactly the same as with Canon "Digital Photo Professional". For INDI FITS file the extracted 5184 x3456 cropped-active-area lies not in the middle of the full-active-area of 5202x3464 pixels but at the side. In Libraw the left and right margin of the cropped active area (thumb) are defined S.raw_inset_crops.cleft and S.raw_inset_crops.ctop and have the for the tested image the values left=168, top=56 pixels. The margins for the active area are left 158, top=52. The difference is the same 10 and 5 pixels.
I have no idea where to place a bug report. Maybe somebody can do that.
Raw size: 5360x3516
Active area size: 5202x3464
Default cropped active area: 5184x3456
Margins active area: left=158, top=52
Margins cropped active area: left=168, top=56
A, Active-area, which is the largest area from which a useful image can be formed.
C, Cropped-active-area, which is the subset of the A Area which many raw converters convert into a useful image. The main reason why C is smaller than A is to provide some extra pixels all around for a raw converter's demosaicing algorithm to use. In LibRaw this area is called Thumb area for some unknown reason.
M, Masked-area, used by some cameras, especially Canons and is used a dark reference.
The blue marked area is where Ekos is extracting the pixels from (cropped active area or in LibRaw terms "Thumb image"):
Easiest fix would be to extract always the full active sensor area. In this case 5202x3464 pixels. Extracting the default cropped active area, 5184x3456 pixels is just a waste. You have to crop the image later anyhow. That is also what other programs (MaximDl, SGP) are doing.