Kazy, maybe you stated this earlier but, what temperature are you running this method at, what's the run time, what are the retention times, what are the analyte curve ranges for each MRM, and where if anywhere is there linearity in the calibration?
Some quick suggestions:
1) Have you checked your water source/for adducts? That is, would you think there may be potential for adduct formation with the analytes.
2) Alternatively, but along the same lines, try making the solutions up in Mobile phase instead of water and look at responses?
3) Use a scouting gradient to find a quick and dirty gradient to run and see if that fixes the problem.
Hope this helps, I'll be looking for the post concerning the questions above.