This is a common problem (that I just finished fixing). It seems to arise in a few different ways. Some people seem to be able to fix it by selecting the default permalink format and then switching back to their preferred one.
In my case, the problem seemed to be that I didn’t have mod-rewrite properly enabled. Once I did the steps in this post, the problem was resovled.
I think I may have also made [this change],
(Category links suddenly started giving 404 errors), but I’m pretty sure it was fully enabling mod-rewrite that did the trick.
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