ISIS seems to have found the lines ok and the fit looks good. I am wondering if there has been some sort of shift between the lamp spectrum and the star spectrum. With the mixed Balmer and lamp line calibration you are using, the lines used for calibration up to 4861 (H Beta) are the Balmer lines in the star and the lines higher than that are from the calibration lamp. Normally the ALPY is very stable but if everything is not quite tightened up, there could have been a shift between the star and lamp exposures. Did you take the lamp spectrum under the same conditions as the star ?
Can you also run the calibration using just the lamp lines ? If there was a shift, we should then see all the Balmer lines shifted, not just H alpha