One thing you might want to check is if there is over spray building up on the platen. I know when I let this go too long, the machine will start seeing the ink build up as part of the material. It may not always look like much, but it might just be enough. Carefully clean it with the solvent cleaner to take the ink up (you might need to do it a couple of times) and you might be surprised that this solves your problem.
Other than that, I have never done the manual alignment. This has always cured the issue for me.