Sorry, Tom and others:I reply late and I did not find the way to change my PDF chromatogram into a picture.
You need to copy the image you want from your pdf and then paste into a paint program (the free Paint progam that comes with Windows will work fine). Then save the image as a .gif file (that is one of the options for file type). From there, proceed per the instructions.
Now, on to the baseline problem. It might simply be UV-absorbing garbage building up on the head of the column and then being desorbed at particular MeOH levels. To test for this, run three "dummy" gradients (no injection). Equilibrate the column for your usual time before the second gradient, and then equilibrate for three times as lonag before the third gradient. Compare the size of your baseline ripples on the 2nd and 3rd chromatogram. If the peaks are larger for longer equilibration, then you have confirmed the cause. If they are comparable, then I would look for something like RI effects.