Things I've noticed.
1) If a stockpile takes quires, then all quires will eventually be tasked with pickup orders within seconds, but none of the orders will be executed.
2) Despite not having any quires in its storage, the Library nevertheless registered itself as having quires in its storage.
3) If a stockpile is generated beneath the quires (and is the only one to take Tools, the quire's category) then the quires are left alone.
4) If 3 happens but there is another stockpile that takes quires, then all the quires will again be tasked with pickup orders and none will actually be picked up.
5) Overlapping areas (chair-based areas + managed areas) causes storage devices in libraries to be counted twice.
Attempted Resolution Conditions:
1) No storage areas take Tools, duplicated storage designation.
1Result) All quires TSKed, no quires moved, but all quires are considered to be correctly stored in the library.
2) No storage areas take Tools, no duplicate storage designation.
2Result) All quires TSKed, no quires moved, but all quires are considered to be correctly stored in the library.
3) Storage area drawn underneath Quires, duplicated storage designation.
3Result) Same as 1 and 2.
4) Storage area drawn underneath Quires, no duplicated storage designation.
4Result) Same as 1, 2, and 3, Though this did work once.
Ex) Take quires to trade post.
5Result) Works fine.
My Inferences
Uh...too many moving parts. It's entirely possible that the reason why this is happening is because my fort has visitors, and they're being allowed to take hauling jobs for those quires (but not actually do them), since for my earlier fortresses in 47.01 to 47.03 did not have visitors to cause this problem.
Reason: I've seen bards move cups and I'm extrapolating rather hard from there.