One issue I get with every track I make is that the negative G values shown in Newton are actually about half of the actual Gs I get on the actual track. i finished an entire track, and the spots that showed around -1 ended up having between -1.8 and -2.2 Gs. Would you know how I could fix this problem?
Yes, this is true. The reason is that newton simplifies the actual problem to a point mass traveling along the heartline (not sure how FVD does it, but as it suffers from similar artifacts, I'm assuming the same way). In reality, the coaster is an extended source, not a 1 dimensional point.
The key concept is one of center-of-mass. The COM of a point source is always at the same location as the point, but this is not true for an extended object. As a coaster train reaches the apex of a hill, its COM is usually lower than would be the case if the train were replaced with a point source. Thus, the train is going faster than newton expects, and the negative g's are similarly higher. The opposite is true at valleys (COM of train is higher, thus train is going slower/experiencing less g's than expected), but since the radius of curvature of the track is typically larger in valleys (...since the train is going faster), the issue isn't as noticeable.
As a coaster designer, you'll need to keep this in mind and create your elements accordingly.