This is a common problem & even though your matting surfaces look good they are probably not matching up perfectly.
I have had this problem in the past on some of my cars and if you don't want a muffler shop make up new header pipes you can cut the pipe in a spot where it is easy to weld in a repair, get a piece of pipe that will slip over your cut pipe and then reinstall.
when you have the header pipe tightened up you can slip the the repair collar over where you cut the pipe and weld in place, you should be able to see how much out of alignment you were by looking at the cut on the pipe.
I have done this on a few cars and have had as much as a 1/2" mismatch in the two pipes after they were cut.
Another repair I've done that seems to work for awhile is to slip a donut in where the gasket is supposed to go and tighten it up, you have to be careful you don't crush the donut.