You mentioned that the plywood was installed over a crawl space. Is your plywood warping due to moisture and humidity? Also what size trowel did you use to install the tile?
I never install floor tile with anything less than a 3/8" mortar bed using a square notched trowel. I know a lot of websites promote the use of 1/4" v-notched trowel installations but I don't know a real tileman that does this (a helper maybe). Why? Tiles suck up the moisture from the thinset very fast and the tiles fail to fully bond with the mortar.