Giedo,
I ran into a similar situation. I have a Canon G6 for "point and shoot"; among other things such as photo copy. I once ran out of CF space and simply "borrowed" the card from the G6 -- it was empty -- and used it in my 20D. When I got home I didn't really notice that both cameras were in synch numberwise. In fact, I didn't find this out until several weeks later when I used the G6 and discovered that the new images shared the same numbers as the 20D. (albeit different lead-in and trailing characters, e.g., img_1234.cr2 vs crw_1234.crw.) Worse yet, I did it twice before what happened sunk in.
My solution, since Canon didn't feel it necessary to let me set my own numbering scheme, is to make sure that I format every card immediately upon inserting it in the camera -- no pre-formatting. (Extra caution is in order if you must change cards in a hurry.)
So do as I did, grit your teeth and just move on. (Or better yet, write to Canon and thank them for making life such a joy.)
Ron