From the changelog of v1.01f:
"Added warning message for when a settlement needs more raw materials"
I find this "enhancement" very annoying. I think it should warn you only when you have no raw materials AND you are not producing them.
In my recent game I have a city with 0 ore stock, producing +5 ore/turn and consuming +6 ore/turn to make tools (+5 -6). Well, each turn due to the ore shortage, I receive 2 messages saying that I have no ore in that city(one per specialist in the ironworks).
I have updated my modcomp "New orders for units" to patch v1.01f ( http://forums.civfanatics.com/showthread.php?p=7870113#post7870113 ). I fixed this feature by altering the following code line (change is in black):
if (bPrintWarning && (getBaseRawYieldProduced(eYieldConsumed) == 0))
in function CvCity::calculateNetYields of CvCity.cpp.
(one per specialist in the ironworks).


I did this with Civ 4, and I would STRONGLY recommend to only get the digital version from D2D or Steam (I prefer D2D, but that's just me). Gamestop (trymedia) does not put the patches on their website, although they do put up the expansion packs eventually.
Sorry.