Mildew & stains on old Lionel

How old are the trains? Do they have plastic bodies and parts?

People commonly mistake a grey-white deposit that builds up on some Lionel trains made around 1950 for mildew. The deposit is actually mold release compound that was infused into the plastic and is migrating to the surface.

If it is mold release compound, it can be removed by warming the parts with a hot hair dryer. The mold release compound will melt, and can be wiped away.
One has to be careful to use enough heat to melt the compound without damaging the part (or shell).

As an aside, I always put my trains in food-grade plastic bags before putting them in boxes. This prevents direct contact between the train and the cardboard. At a minimum this prevents box rubs. Do not seal the bags. In fact, I often punch a few holes in them. The idea is to avoid trapping moisture.

Its prewar, tin plate cars & die cast steam locos. The locos are worse off than the cars. Because of the shiny paint, the cars clean right up for the most part, but the black paint on die cast on the locos holds marks from the mildew. It seems to be growing mostly where it does touch the carboard, I'm guessing it isn't dead inside the boxes & its growing back when I put them away. I'll clean them again & put them in bags or wax paper & see if that helps this time.

That might be zinc rot on the locos... Can you post pics?

Naw, its mildew on top of the paint, it wipes right off.

I have a Lionel 260E with the same issue, but I wasn't going to tackle it until after the engine comes back from being rewheeled. However, since you're struggling with the same issue, I tested my plan tonight. I used some of the b-Gone Cleaner from Mega-Steam. With some rubbing it removed the mold in my two test areas on the tender. I will monitor it for a few days and see what happens.

CW is absolutely correct.  Heat is the only thing to STOP it, but you have to do it carefully.  As he mentioned, a hair dryer is sufficient, and if done correctly, it won't come back.  Also agree with his method of storage too.  You won't go wrong.