After testing a little bit, I think that the reason why you got less points for "doing better" is because a getting sick!! note doesn't mean you got all the points.
Basically, the max amount of points you can get on a note is 500, which is a (frame perfect?) sick!!.
But you can also get a sick!! note, and only gain 413 points (that's the lowest score I got for a sick!!, the lowest is probably 401 i'd say), or even 499.
This is I think what happened, you just got more "bad" sick!! notes on the "better" run.
You can try to see this for yourself by playing the very first part of Satin Panties on easy mode.
If you get less than 2500 points with 5 sick!! notes, then you actually weren't truly perfect.
