Actually, 3.3.5 fixed our problem but it introduced the file sync problem that led to even more problems. Your 'do not have permission to view....' problem may just have to do with the permissions on each directory. If your Intranet restricts access based on roles, you may have to give that role permissions to view that directory. 3.3.6 fixed all the file sync and directory problems.
Just another note, 3.3.6 introduced a major bug for us. Since you are using it in an Intranet application, you may been creating your own modules. If so, the 'Add new module' function on the 'host/module definitions' page is totally broke. You can't manually create a module and then add definitions, etc. We fixed ours by commenting out some erronous code in the .vb file and then recompiling DNN. We replaced the dotnetnuke.dll with ours and everything is fine. This will work until they patch 3.3.6 or until the next minor upgrade. To read more about this, go to here
Have fun!