I have same exact problem as https://magento.stackexchange.com/questions/58201/configurable-product-not-showing-in-magento.
Make configurable product "In Stock"
Use "Quick simple product creation" to generate simple products "enabled" "not individually visable" "in stock" "qty > 0"
They do not show up in "Super product attributes configuration" section
It appears that they do not get 'associated'
I have tried regenerating all indexes, flushing all caches numerous times.
Once in a while if I start from scratch, the associated products will show up, but 5 out of 6 times ... it won't work.