I came across a conflict with the WP Events Manager Plugin (EM) when it is working in Multisite mode. Let me set up the situation.
With EM in multisite, you can network activate the plugin so that each sub-site can have its own events, and also aggregate all events across the network into a list that can be displayed on the network home. I noticed that when this feature of (EM) is in use, and when W3TC is also activated, the network list (on the network home site) will not link to the subsite but try to link to an event on the network home site (which doesn't exist). For example, if i have an event called test event 1 on a sub site called My First Sub-Site, it should link as so: http://mysite.com/my-first-sub-site/events/test-event-1/. However, when on the network home site, the link that is created is: http://mysite.com/events/test-event-1/ which does not exist, and therefore sends the user to a 404 page.
The EM plugin author was kind enough to look into the issue (before I went through deactivating plugins 1-by-1), and could not find any reason for this to be happening. When I deactivated W3TC everything returned to normal. We were wondering if W3TC had problems with get_blog_permalink since we cannot seem to work through this problem.
Thanks for your help!