Only thing I could think of this being is conflicted .fho groups, though I'm not sure. I used to run into this issue myself.
When you download a map, before you move it into exports, can you see the .fho files in there? If you can't, then I really have no clue what's going on.
What I had messed up on was overwriting files - when you move everything into exports, do you overwrite similar .fho files? If you do, that may be what's causing your problem - you want to keep both your old and your new ones. Though it doesn't seem like you're doing that, it's worth looking into.