Hi John,
That sounds a bit odd. Can I check that the spectrum definitely calibrates successfully. If you hover the mouse over the spectrum plot in tab 5, then do you see sensible wavelength numbers appear for the cursor position in the bottom left of the screen?
Also, you say you are not using the Alpy calibration module. Are you using an A type star, or similar star with prominent hydrogen lines to wavelength calibrate your spectrum? Or are you using a neon lamp source, just not the one that comes with the ALPY, in which case you may be able to select the “ALPY 600 (with calibration module)”.
Cheers,
Andy