There is nothing inherently built into Plotter that biases it in any direction. It is a simple measurement and analysis tool. It applies standard sensitometry methods for the most part. That said, it is a closed-loop system inasmuch that you target your negative contrast to your paper tests (via the ES value). If you are finding that your negatives are softer then I suspect it could be any of a number of things. If everything matches up you should not need to boost your ES to match your paper as your paper tests tell you what ES they require.
Some examples of things that could cause this (not a complete list):
1. Your paper tests are not properly calibrated to your film tests. This could be an issue since you get your negatives exposed via VCS and you do your paper tests yourself. There could be a mis-match somewhere. They key here is to get your setup to match VCS's.
2. Your light meter does not match the one being used to produce the film test exposures. It could also be your metering technique (i.e. you have placed your highs incorrectly leading to softer contrast negatives).
One thing you might try is to set up your own film test using the same light source and meter used for your paper tests. Just do one sheet of film and develop for a time that should give you a curve with an SBR of 7. Then add this curve to your existing Plotter film test and see where it falls. If it doesn't fall near SBR 7, then your setup isn't matching what VCS does and this is likely affecting either your negatives from the field (due to your light meter) or paper tests or both.