I suggest the use of the scientific method, otherwise known as “guess and test.” There have been several good ideas presented thus far, poop pyramid, roof leak, backup, etc., but you will never know what is causing the issue, until you run simulations.
The easy way is to take it in for service and pay the man. Lots of good people let the pros handle issues pertaining to black tanks. However, there are those individuals who are, ah, frugal, and relish the chance to play detective and are pretty good at solving RV holding tank problems.
If you are in the latter category, you may want to start by emptying the holding tank, while making absolutely sure it is dry. Next, determine if you have a gunk buildup. If so, by using a stick or dowel, approximate the displacement of the gunk and compare it to the volume listed by the manufacturer. Angle the probe, if necessary and spin in a circular motion.
After ruling a pyramid as in or out, use the stick to measure the depth of the water in the holding tank, while running a scenario on the most likely culprit, first. Then try the next possibility. You do have some insight as to where to start, after rain caused a rise in water level. Where does rain come from? Up! I’d start there with a hose and a five gallon bucket.
For example, tape off an area so that the test water is only applied to a very small space. Fill the bucket and pour it on the site. Test for effect or more precisely, how much of the five gallons can be found in the holding tank? Give the matter a half hour, because leaks sometimes run slowly. Also, it is important to be meticulous in only applying water to the target area, especially since liquids don’t always run straight down hill.
Importantly, all roof penetrations should be suspect, including doors, windows, and awning attachments. Search Phred’s Poop sheets and “Handling Moisture in RVs.”
After five RVs, I have come to the conclusion that loose or the wrong type of caulk is the most likely suspect for leaks and this is especially true on antenna installations and above an entry door that has pulled away from the wall over time.
This situation can be remedied and if it were me, I would not go the storage area route. An experienced RVer would not let this test of his integrity be settled without a fight. And the only way to get experienced is to fail until you pass.
Good luck.
