Yes it makes a difference. I think you cut the inside of the channel closest to the fence first. Then move out. If you cut the outside first then move in the bit will try and self feed.
or, unless you have a flat saw blade, hog it out first with the table saw, a mm or so from the final width / depth, then use the router for the clean final cuts.Do you have a table saw? If so I'd use it to male the dado even if you are only using the blade. The second way would be to make the in and outside costs then use the router to hog it out.
stopped dadoes are done easier free hand using a guide/jig and a two pass cut.....Thanks for all replies.
The example I gave was not an actual case for me, but I have often wondered if there was proper order. I think Cherryville Chuck mention of self feeding is a good reason to do the closest cut first.
I do have a table saw and dado set that I generally use for dados. However I have encountered this situation several times making stopped dados, not to the extreme in my example but maybe trying to make a dado for "1/2 inch" plywood.