Okay, after thinking about this some more, I realized that the 45 degree angle of the two pieces joined to make the rectangle is the same kind of seam I get when I join pieces of binding diagonally to make longer lengths. After playing with some scraps, I think if I cut the pieces (that I had cut as 2 1/2" squares) as rectangles, about 3 1/2 x 2 1/2, I can join them to make the pieces I need (I'll cut them to the correct length after sewing). At least, I think so!
Maybe I can still salvage the rectangles I have already cut, but will have to find other uses for the 2 1/2" squares--maybe use them on the back side of the runner.