I'm seeing similar issues with my 6.4 implementation. I created a local AEM test user and put that user into the content author's group. Then validated that the test user was granted read access via the content author group.

However when logged in as that user the CRX console does not show the folders in which the user has read access to:

There is ONE exception. If I add permissions to "home" withing user admin, that then shows up under CRX/DE but no other folders with the same permissions do.

The only solution I have found is that in order to access crx/de a user must be in the Administrators group, which is not a good solution for content admin access.