Kaleea - that "inability" of midi-recording to notate the music "properly" is because most human beings play an interpretation of the written music, not the exact written music.

Since humans aren't robots, and since notation is itself inexact, it's rather difficult to create a program that will understand what non-exact (live human) playing means. Cakewalk does have a "quantize" button, which will hide the sloppy playing for printing purposes, but you still have to play rather close to the timing needed or the program will show your mistakes.

Playing to a metronome is really difficult for me, I go all over the place where timing is concerned. This is why when I want to record something close to in time, I create a rhythm track at the tempo I want in Fruity Loops first. Then I export that to audio and put it in Cakewalk, then record the midi track along to the rhythm. It works pretty well.