I don't know what model of incubator you have, whether it is forced air or still air, what your water reservoirs look like, what type of paper you used, or where it is positioned.
Humidity is controlled by the surface area. Volume and depth don't matter, except as far as how long you can go before it all evaporates and you have to add more. If the paper is blocking the water in the reservoir, it could be reducing your humidity. You may have very high humidity under the paper and very low humidity above. If you have a forced air incubator, you may be altering the regular air circulation paths. If the paper is touching the water, it should be absorbing the water and increasing your humidity, depending some on what type of paper it is. It is also possible that the paper is absorbing the water and the humidity will eventually come up and stabilize. If it has been a while, I suspect you are reducing the effective surface area, but I don't know.
The instructions with my Hovabator 1588 did not recommend to put paper or anything down to help clean up, so I don't alter the design of how it is supposed to work. Besides, the wire to give good traction to the chicks feet and the plastic reservoir clean up pretty easily.
Good luck! I hope it works out for you.