If the sky lines are in the right place in the QSO spectrum, your calibration must be good so perhaps there is something odd with the pro spectrum you are comparing with. Can you post the file you used and I will compare with the version I have. You could also download my spectrum from the BAA database and try overlaying your spectrum on it.
I find once the pixel size has been tuned, the automatic calibration function in ISIS using the NeAr lamp works very well with the ALPY600 but I have not yet found a way to use it with the ALPY200 as the lines are too blended. I still use it though to measure the slant/smile and use the strong 5852.49 line as a fixed reference between observations, setting the X position in the calibration tab so ISIS uses that to compensate for any shift. (the constant term in the dispersion equation)
Cheers
Robin