In first semester of my 3rd year, I had 2 classes with the same professor so I wanted him to write me a reference letter for optometry school. I asked him at the end of the semester (Dec 06) if he would write me a reference letter for my application in the following year, being this year (fall 07). I hunted him down on the first day of school of my 4th year this past September and asked him if he remembered me and if he could write me a reference letter. He said yes and completed them in Oct 2007, a year after I took the two classes with him. Thats how I went about doing it...
Also, after speaking to another professor who wrote me letters, he told me he does 125-150 ref letters a year, and he does them all in "2 sessions" - I'm not sure that that means. So don't worry, professors do reference letters all the time and you could probably just speak to your prof about your situation and see what they can do for you.