This is just how it is. If you really want all to have a similar level, you'd probably need to set them all to 127-127, then figure out which is the quietest, and then adjust all levels downward to match that quietest one. Obviously, this is a big hassle. I did this with a subset of my patches that I often use in one set. By doing so, you do of course slightly limit the volume dynamic of the "loudest" patches.
By the way, I am much more enjoying my rev2 since I have my L1, R1 and L2, R2 going into a little mixer, so that I can make immediate adjustments to levels of the layers/parts. This is not really a solution to the problem you describe, but it makes it much easier to work with.