I am not entirely sure of your question, but I'll try.
First thought: Be sure your inlet maintantanace is up to date. A leaking septum adds all kinds of variabilty that you don't want.
Now that we have addressed the easy one to fix, on to the harder ones.
If your question is variability of the area of the internal standard and it shows an relative standard deviation of 10%: I would look at integration conditions to be sure the peak is integrated the same way every time. I would also try using a 1 uL injection rather than 0.5 uL. If everything is optimized as good as you can get it, 10% RSD on the internal standard area may be as good as you will get. I would try things like a slightly hotter inlet -- but with water, you quickly run into the risk of your expansion volume putting analyte out the septum purge vent or back into the inlet plumbing. A hot inlet with a pressure pulse could work as well - but that takes some tinkering and may not get you any benefit.
If your area ratio of analyte to internal standard shows a 10% standard deviation, I would look at the same issues. I like 5% RSD's on methods. (But if I am doing trace analytical, I may be happy with higher RSD's - to get some kind of result at ppb levels.) Run five injections of the same standard - mid range in your curve - one after the other and let me know how the areas vary for internal standards and a couple of analytes - one early and one late. I may ask you to post chromatograms.
Unfortunately, this is one of those problems I solve best by sitting in front of the instrument, and examining all of the parameters and talking to the instrument (It does not talk back - but I feel better).
Don