Did you have a set nick point inside the D-loop, or did you just eyeball it? Is it possible that, even with a set nock point, that you put the D-loop on backwards, meaning that you used to put the arrow above, and now it's below, the nock point? Another possibility is that the D-loop was incorrectly tied before (both knots on one side of the string), and now you have it right (one knot on each side of the string), or vice versa.
When all else fails just start over from the beginning with however you tune your bow (paper, walkback, french tuning, modified french tuning, etc.). Let us know any problems or questions because there's plenty of guys on here willing to help.