This should be fixed now. The problem I introduced and have resolved is clicking "I've checked all of these" in succession. That is, on a page of Newest Nodes that was loaded as a result of clicking "I've checked all of these", clicking "I've checked all of these" (again) would keep the last-checked date the same. Reloading Newest Nodes for any other reason would break the cycle and fix the problem.

There is still the race condition in the node cache that can cause the "I've checked all of these" to be ignored on rare occassions, usually when you are getting a lot of votes on nodes changing your XP.