It could be outside water coming in from the transom or thru hulls or from the engine cooling system or the onboard water system. Need to do some more diagnostics.
Your probably not going to notice a big difference in any of those to what your hull color is. If the areas you are doing are relatively small, I doubt you will even notice a difference.
If you launch your boat each time, you definitely need to prepare a checklist of "do`s" while in the staging area. The drain plug is the most critical, second being removal of the transom straps. Don't get in a hurry.
I`ve have never really worried about it. I just put it away with whats in it at the time. I do overly treat the fuel in there with Seafoam and Stabil products and tape off the tank vent on the exterior of the hull to minimize the draw in of new cold air. Each spring, I top off and fire up, I`ve...