Not sure if you are having the same problem as me but I will let you know what mine is and let you check yours. I have one of those metal sheds that you buy the kits for at home depot. My bantams are in it. My fiance originally got it as a tool shed and built a very good floor. It never stopped getting wet on the floor when it rained so when we moved and brought it with us he gave it to me. Well I finally figured it out and we have tried to fix it to no avail so far. He said he is going to use roofing tar when he gets a chance. When he built the floor he made it bigger than the structure so the structure sits on top. However the floor comes out an additional 1-2" on each side. When it rains the water seeps under the structure and onto the floor inside. It is caulked very well all the way around inside and out but it still leaks.
From your pictures it looks like that might possibly be your problem as well. Just a thought. I know you have a lot of other things to check for as well.
From your pictures it looks like that might possibly be your problem as well. Just a thought. I know you have a lot of other things to check for as well.