Peter,
Thank you again for your thoughts -
1. The theoretical amounts should be right around 18.5 ug/ml for both Drug A and Drug B. In a single sample set run: the First check solution showed Drug A at 17.9 and Drug B at 20.0. The second check solutution of that same sample set showed Drug A at 19.7 and Drug B at 17.5. The check solutions are from 2 different vials aliquoted at the same time. In other words, first the "A" was low and the "B" was high. The very next check from a different vial showed the oppocite: the "A" was high and the "B" was low.
I think you got me going down the right path. So I injected 3 times from another two different check vials.
Check Vial One was: "A" 20.3, 20.5, and 20.3 ug/ml and "B" was 17.2, 17.3, and 17.4. ug/mL.
Check Vial Two was: "A" 22.6, 22.7, and 22.7 ug/ml and "B" was 14.9, 14.9, and 14.9...
3. The 65% acetone is fairly strong, but it was decided upon before I got here. My understanding is that this solvent concentration combined with the shaker table speed and heat produces elution results that meet the regulation requirement of less than 20% elution before the first timepoint and greater than 80% drug elution at the final time point... It's possible this could be treaked maybe a lower solvent concentration with more heat on the shaker table... Tough to say at this point. But you say the peaks would be badly shaped right? I would see shouldering or spliting maybe?
5. I think I understand - basically if the check solution peaks were huge compared to the sample peaks this could be a saturation issue? In any case, the peak areas are about the same in this situation AND the peaks are going kitty-whumpus (different dirrections).
6.

Well you bring up an excellent point. I think I may have raised this question at one point - the thinking was that it had been a problem in the elution vials, but not the HPLC vials with the old solvent... - but maybe the same interaction that was causing the polymoroph issue in the Methanol was also slightly protecting the drug from sticking to the glass - the acetone elution drug samples might be "stickier"... Only one way to find out. Maybe I will try TEA coating some of the HPLC vials today and see how we do.

Especially, *Especially*, since the two control vials with the 3 injections each were repeatably different. Oh my...