I did not try, but logic would suggest that if a user has rights on a parent folder, he automatically has rights on a child folder. Did you verify that it is not working like that?
Sync db and file system makes sure that all filenames are also in the db. The filenames in the db are used in the url control that you can find in a lot of modules...
Just out of curiosity, how many files did you copy to your portals directory. There are some problems if you have more than integer.maxvalue (2147483647) bytes, or 2 GB in your portal folder...
cheers,
erik