Invalid permissions in Document Library

Hello,
Somehow we managed to get invalid permissions in Document Libraries on our Sharepoint server.
Our Farm is a brand new 2-tier setup (1 server is database, 1 server is AD, IIS and Sharepoint itself).
We added users at the same time as we copied our data to sharepoint (through the Explorer).
We have a subsite for our "Production"-employees, each Employee will make products for a set of customers.
Each Customer has his own Document Library; this is where we put contracts, project-documents, designs, everything.
So, we have Document Libraries called something like "Customer A", "Customer B", "Customer C". "Employee 1" works for Customer B so he will get access to Document Library  "Customer B". He does not work
for Customer A or C, so he does not get access to those. We have about 60 customers so we have about 60 Document Libraries.
After we configured this and everything was set up we got complaints that our Employees could see (in the App-Treeview) large sets of "Customer"-libraries that they shouldn't be able to access. If they would click on it, they get an error saying
"Sorry, this site hasn't been shared with you.". Also, other sites which should be invisible are indeed invisbile. I have a mix of valid and invalid sites. 
So to continue the example: Employee can see 2 Document Libraries, "Customer A" and "Customer B", where I would expect he would only see "Customer B". "Customer C" is correctly hidden. When I look at the settings in
"Customer A" he has no access. But the customer is in the TreeView, nonetheless.
I went out to investigate. When I check permissions I can see the user indeed does not have any permissions. That is good.
I wrote some code (in C#, using Sharepoint.Client) and I found out that Document Libraries are working correctly (Customer C) only show "EmptyMask"-access for a user. And for sites that do NOT work correctly ("Customer A") I see the following
access:
EmptyMask
Open
BrowseUserInfo
UseClientIntegration
The "Open" permission would explain why the item is visible. It looks like these are inherited from the Site-settings (am I right?)
Now I don't know how to correct this situation.
I tried writing some code in C# that detects this invalid setup, but I can't find a way to only change these Permissions without creating new Security Roles and such. I don't want to create security roles.
I have googled for solutions, but I cannot find anyone with the same problem.
Anyone can give me one or more pointers?
Thanks in Advance!

Two points. 
Are you logged in as an Admin or Site Owner?  Security Trimming in things like Site Contents will act differently for Admins than it will for regular users
Enabling the checkbox you did in the document library should automatically add it to the Quick Launch unless you have custom edited the quick Launch.  If you have then it takes the custom editing rather than the dynamic list created by the checkbox.
By default users will see the document libraries they have access to.  The problem is that you've started customizing things and there is no easy way to get back to the default after you do.
Paul Stork SharePoint Server MVP
Principal Architect: Blue Chip Consulting Group
Blog: http://dontpapanic.com/blog
Twitter: Follow @pstork
Please remember to mark your question as "answered" if this solves your problem.

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