By default NCPlot does store all variables on exit. However, you can turn this off on the Preferences dialog. Just uncheck the setting that says "Save Variables On Exit". This also disables re-loading of the variables on the next startup.
Can you explain in a little more detail what it is you're seeing? Do you only see the problem after first starting up NCPlot, or is it in any G84 block that doesn't include an "R" value? How does your control handle it?