The question I have is did you have the density differences using the same "lot" of paper with different inks. You opened in saying that it was with different inks. Different inks can and will certainly give you a different numerical density number, even with the same lot of paper. The lower density black numerical value in fact may look darker, jetter, and denser than the higher reading density print.
Why?
This is due to the particular characteristics of two inherently different ink formulae. Numerous factors come into play when you look at 2 different black offset inks, if you have the privilege of knowing this. Usually you don't because they are competitive products. This is where you might need D Ink Man to pay a visit. Some of the explanation can be given here. Two blacks can certainly and most times due have different carbon containing blacks which will have an effect on the visual density due to the jetness inherent to a particular carbon. The vehicle systems within the formulas have a profound effect also. The job of the well versed ink formulator is to utilize a good wetting vehicle system that enables the carbon black pigment to be completely wetted, and to surround the individual pigment aggregates. By doing so, this exhibits the best properties such as gloss, strength development and transfer capabilities to name a few in the finished ink product.. Also, the grinding median used to grind/wet the pigment is a huge part of the accomplishment. There are many ways to achieve this in the ink making process. Three roll mills set to the correct psi for dispersion and grind are one. Another would be a bead mill, that achieves the pigment wetting by a combination of time, rotary shear and temperature. The bead or ball size, as well as the condition of them are other critical factors in seeking a maximum, properly wetted pigment. This also applies to the other numerous pigments used in making printing inks.
So in summary yes, the phenomenon of densitometrics measured can be a reality in a dynamic sphere such as yours versus what we see with our eyes as simple human visuality. I will not include dry back in the discussion here, as this may only cloud the points. That is for another discussion.
Hope this provides some understanding.
D Ink Man