Hi John,
If you use the “no ALPY calibration module” setting in ISIS it automatically finds and uses the first 7 Balmer lines in the star spectrum, plus the head of the telluric band at 6872A for calibration. Only the resulting calibration fit coefficients are transferred into the dispersion window so you can use them for subsequent calibration of further spectra (using the “predefined dispersion equation” option). The list of lines for manual entry shown there are just what happened to be left over from a previous manual run. If you delete them all for example before making the calibration you should see that only the coefficients are filled in after calibration.
HTH
Robin