Since installing WordFence, I've noticed permalinks to my blog posts get broken regularly. I use a standard method - http://www.jasondunn.com/%postname%/ - and after changing the permalink type I confirm that it's working. A few days later, those same links are 404 not found errors. The permalink configuration has not changed. Changing nothing else, I'll toggle from one permalink type to another, click Save, and my posts work normally.
I disabled WordFence for about four days and the permalinks kept working, and since re-enabling it I've seen them break again. I run very few plug-ins, none of which are new in months other than WordFence, and this problem started shortly after I installed it. So it seems likely that something in WordFence is causing this.
I haven't been able to find mention of this anywhere as a known issue, so I don't know if there's something weird about my fairly stock install of WordPress...