Otto42,
A lot of people have been having this problem. I hoped the latest update would solve it. I have been receiving 404 errors from my links for over a month now – all of my links, including comments, post pages, page 2, etc. I have written about it in this forum and have monitored other discussions. No solutions have been offered that I have seen. I am not using a custom permalink string.
Do a search for 404 and links and you’ll find some of the threads about this problem.