It's not clear exactly what you mean here. Do you mean to say that if you make 10 exposures of exactly the same subject under the same lighting and the same camera settings, each one of those exposures will scan differently with that combination of the V600 and Vuescan you are using?
Or do you mean that the images themselves are of different subject matter or different lighting? In this case, you have to expect the density and colour balance of the negatives to be different from each other, and therefore each needs to be adjusted in Vuescan (or any other scanning software) individually, and the adjustments can be large, depending on how different the photo properties are.
All that said, scanning negatives is not as straightforward as scanning positives, and the scan software can either add to or subtract from the difficulties you are having. While Vuescan itself may do an adequate job, I would nonetheless suggest you test for this variable by downloading a demo version of SilverFast and see what you can achieve with their NegaFix solution (in the software). This will cost you no money, only a bit of time, and then you can assess whether there is a consideration of software in helping with the issue.