It's a long-standing caching bug - in the old days, there were lots and lots of items in the /tools/flagged queue, and we hid items you had already flagged (or taken action on).
Now, most posts that would have been shown in /tools/flagged are sent straight to various review queues, so /tools/flagged stays a bit lean.
I'm just going to show the items you have flagged in a grayed out (or semi-opaque) styling, so you can see what you've already acted upon, and I don't have to make some crazy, per-user caching structure that stays in sync with flags (especially since we want to remove /tools/flagged in favor of review queues).
So, next build will push out the above changes; here's a screenshot illustrating them:
Gone is the random sorting of /tools/flagged - it will now be sorted the same as the mod queue, which is by most flagged post, then oldest flag. Also, if you've already flagged a post in the /tools/flagged queue, it will be sorted to the end of the list and grayed out, with some explanation of why you can no longer interact with it.
Thank you for being the straw that broke this camel's back and made me fix this bug :)