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.