That Ctrl-click tip is huge! It was not intuitive in the interface. I will add text there to help the client know that they need to ctrl click each category area they want their product to be listed under. My assumption was that if you selected a sub category of a parent category it would relationally (and automatically) be part of that higher category.
I just did the ctrl click trick for a three tier category product and it worked for all three.
Thanks again for the post!