file system rights

We are having trouble with file system rights with many of our applications.
We are assigning rights to the application distribution folder through the
application. It shows that there are rights but the users do not have the
rights to see the folder when the application deploys. Some locations work
ok some don't. Once we give rights outside of the application to a group,
user, or OU then it works fine. Does anyone know how to fix this? We don't
want to give blanket rights we only want to assign them when the application
installs.