OK, when I added the admin_log at the increment I found that the increment is run twice, so I took a look at the access log again. It seems that every request is doubled, with a two second delay (which is why I didn't notice it when I looked at the log for the production site). The second request increments the counter without it being shown, since it is the first query that is sent back to the browser.
It seems that I get every request twice, or at least the ones to showflat/showthreaded... If this is true it means that I'm using way too much cpu and bandwidth than necessary... Not sure if this applies to all requests though... Need to check on this a bit more.