Hi Katie
I am starting to get as puzzled as you are. Early on you confirmed that you were seeing positive deviations from linearity - in other words that the higher concentrations gave bigger peaks than expected. Then in your 11 March post you give peak areas that are SMALLER than expected for higher concentrations, and SMALLER in the presence of samples. This is easy to explain by detector overload (which is what the Agilent rep was telling you) but all of the other suggestions on the forum will fix positove deviations, not negative ones. Positive deviations are trickier to explain and more difficult to troubleshoot.
In your 5 March post you referred to direct injections being inconsistent. I thought that you meant injections of liquid samples direct to the GC inlet (in other words with the P&T disconnected). From your second to last post I now see that you were loading the standards etc into sample vials and then (presumably) running them through the P&T.
If you really do have positive deviations from linearity you need to isolate the various components of the system to localise the problem. Disconnect the P&T and make liquid injections (split) preferably with an autosampler, direct to the GC inlet, with the same quantities of each analyte going onto the column as you would have for your P&T calibration curve. If you still have the non-linear response the problem is in the GC-MS, if not it is in the P&T.
Over what range are you calibrating (in terms of mass of analyte on the column)?, and what are the compounds in the standard ?, is the strength of the effect related only to the concentration (mass), or are compounds of different chemical class affected differently ?
Peter