I've given up using metal terrain models. Good as they often look, they just don't seem to hold paint. There is an inevitable amount of jostling in a box, and paint chips off the things much faster than off resin, or even plaster or ceramics (my Chinese pagoda started life as a hideous fish tank ornament).
I don't have any metal terrain models, just resin so can't really comment. But when we paint metal objects at work, we first use an acid etch primer that binds itself to the surface. Without this the paint comes off too easily. Sounds like this is the reason your metal terrain wears more quickly.
Metal also has the disadvantage that it's heavy volume for volume. However, in the interests of preserving your existing items might I suggest layers of bubble-wrap? I use the micro-bubble variety - cheap and effective.
I've already given them away.