That keyboard explains it then. And btw...they're so stinkin' cheap these days....buy a weighted keyboard. You deserve it. :) Also, the fact that all the notes are 60 explains it. I've never really studied mine, but I've noticed that no key in a chord is the same velocity, which makes sense because your fingers touch at different velocities. The melody should be the loudest for one. Otherwise, I'd have to look. I can't imagine editing those in PRV though. :( In the meantime, perhaps pulling them all down a bit more would do the trick.
As far as lining up to the beat...I've never thought about them not actually being on the line. You can always hit input quantize and set it to 1/16th...that will save some editing.
But really, not everyone will even notice that.