I've been running duplicate samples through an older Varian 3800 GC with a Saturn 2000 MS. THe only detector is the MS. I'm getting wildly variable TIC peak areas from replicate injections. I'm seeing 20% plus variability and the injection volume is reproducible to within 1%.

Anyone have suggestions on where to start troubleshooting?

The column pressure/flow seems stable although I am changing the split ratio mid-chromatogram from 500:1 to 50:1