I upgraded my multiuser site from 3.4.2 to 3.5.1 over the weekend. The first problem I noticed was that when I ran the updates for the individual sites, the list of site names all had the url of the base site. I chalked it up to some not-critical bug since the sites all seemed to work okay.
Later in the day I went to work on something and noticed that when I opened the list of sites by hovering over the My Sites menu on the Toolbar, the list was had the correct number of entries but every single entry was the site name (and linked to) the current site I was working on.
I did a bit of debugging to see if I could figure out the cause. The best I could get to is that when the list if being built, for each individual site in the list, the database prefix is pointing to the current site instead of the site being referenced for the list. Even if I do a direct call to $wpdb->prefix immediately after calling switch_to_blog (which returned "TRUE"), the result is the prefix of the blog I'm on, not the one I switched to.
I have two other multisite installations that are not experiencing this issue. The only thing I can point to that is different is that this is a subdomain style multisite, while my other multisite installations are subdirectory style.
I'm not really convinced that this is a subdomain multisite bug, but I have not the time today to test that theory out. I suspect that something else is driving this, but I don't know what. I disabled all of my network activated plugins, but the problem persisted even while I was on the network dashboard. If I remove the plugins directory, the site hangs and I'm not sure why yet. I plan to do that again tonight to see if I can learn anything further.
Bottom line is that it seems like the wpdb->prefix is not getting changed during a switch_to_blog, and I was wondering if there have been any similar issues seen, or some guidance I can get to figure this out. I'm guessing that going to the main blog dashboard, resetting the theme to one of the default themes and clearing out the plugins might at least show me if the problem is present then, which I will do tonight. But any other thoughts would be appreciated.
Oh, and this happens if I go any of the site management pages as well. The All Sites page on the Network Dashboard looks like it's working, but the "Visit" link for each blog points to the main blog instead of the one it should.