I had intended to reply earlier to this but it slipped my mind.
The software of most scanners, and all professional scanners that I have used, is designed to give correct orientation of the image file when the emulsion of the film faces the CCD. This makes sense because this is the cleanest look the CCD can have of the image on the negative.
For some reason Epson scanners give the correct orientation when the base side of the film faces the CCD, with the emulsion up. This is ass backward to what one would expect, and of course different from most other scanners. I have never read an explanation for this but it may have something to do with flare that you might be with the base side of the film facing the light source, as was implied in a previous message.
If you use the BetterScanning holder with AN glass my advice is to fluid mount the negative to the smooth side of the glass, with the emulsion facing the CCD and the base of the negative in contact with the glass. The AN glass, which is now facing the light source, will smooth out the light and prevent flare.
Sandy King