Most boats have water trapped in the hull stringers below the sole. That water comes from various sources like sea spray, plumbing leaks, water spills, washdowns, wet bathing suits, rain leaks, Cooler discharge, etc. Some of that water gets released when the boat is set in motion. It is very common for a boat that has been pulled up a ramp and trailered to show released water in by the stern of the boat and in the bilge. The amount of water trapped below the sole over a period of time is usually significant consisting of multiple gallons. I'm not saying you do not have a rain leak that maybe contributing to the water trapped below the sole. What am saying is that the sudden appearance of a large amount of water is very likely water that has been accumulating over a period of time under the liner. You can test it by removing the water you found and drying the bilge and the stern locker and hitching up the trailer and taking it for another spin over some rough road to see if more water is released. Do not drill holes in the liner as some of this trapped water will be fouled and the awful smell can be released into the cabin. I do not have a solution to the water accumulation because as long as I don't feel any smell it does not bother me and I let the bilge pump discharge the water. I am careful when cleaning the boat not to use too much water and every once in while I will take the boat out heel it it sharply in opposite tacks to shake some of the water out. I have seen people pour a chlorine solution and then take out the boat out and induce motion to mix the waters.