I use the router and straight edge trick,too. But one thing is different in my process.
The straight edge is clamped to the first piece and edge routed. Leave the straight edge in place and clamp into position the second board so a gap 1/16" smaller than your cutter diameter is between the two boards. Now run your router the opposite direction of your first cut jointing the edge of the second board. This will leave a mirror image on the second edge and your peices will mate perfectly. Any irregularity in the straightedge will not matter as the defect will "key" into each other..
A couple more tips... make sure to run the same spot of the router baseplate against the straight edge for each cut. One smooth motion and speed the entire length of cut will also produce better results.