Why is it that when I try to make my midi, the measures are played at different times? The measures don't exactly line up together with each other on the grand staff.

It's becuase you probably put somthing in wrong.
I did exactly the same thing and come to find out
I had missed some rests and forgot to change the note
lengths. so to fix it just find where it doesn't line up and go
through it to find the mistake.

Lightning Gem

Try using 'automatic bar line'. You have to regularly use it otherwise the staff will look weird.

ah, I see, thanks n_n