The chemistry of aqueous corrosion inhibitors is complex and the mechanism by which molybdates inhibit corrosion of ferrous metals is uncertain. According to a paper presented by Susan Rey and Gary Reggiani at the 2005 AWT (Association of Water Technologies) Annual Convention, molybdate is classified as an anodic oxidizing inhibitor and is not effective in the absence of oxygen. It is believed that molybdate ions react with ferrous ions to form a non-protective ferrous–molybdate complex which, in turn, is oxidized by dissolved oxygen to form an insoluble and protective ferric –molybdate complex in combination with ferric oxide. It is also hypothesized that molybdate strengthens the outer most hydrated iron oxide layer by hydrogen bonding to hydroxide groups on the surface. This imparts a negative charge on the surface which "repels" aggressive chloride ions preventing them from reaching the surface. Rey and Reggiani say that "from a practical standpoint, the absorbance of molybdate onto the outer hydrated iron oxide layer means that when molydate is fed to a poorly maintained system containing old corrosion products, molydate will be consumed, leaving the water treater wondering how it disappeared. Therefore, prior to using a molybdate based treatment in a fouled system, the system should be cleaned to remove existing corrosion products. Another implication of the molybdate mechanism is that oxygen must be present, or another oxidant such as nitrite, if a molybdate treatment program is to be most effective." Perhaps this explains what you are observing in your system. Your best bet might be to contact a third party specializing in water treatment to get advice on your specific system.