I have an issue similar to these:
URL authorization failed for the request
IIS File authorization failed for the request
I am running several similar web sites on IIS 7. I am testing with Firefox, so that I can act as users other than me.
I have been doing all my work on site 1.  I can log in as network users administrator and sys\bob.
I am now working on sites 2 and 3.  I can log in as administrator just fine.  The problem is:  When I log in as dom\bob, the initial log in is properly authenticated.  On all subsequent requests, dom\bob is rejected for either a file or a URL authentication failure.
The Application event log entries are materially similar to those quoted in the linked issues, except that the custom event details section is empty.
I have checked the web sites in IIS Manager and found no differences so far.  I have confirmed that the web.config files are identical, except for site-specific information such as the connection string.  I have verified that the folder permissions are correct as far as I have looked.  
Specifically on permissions:
The <authentication> mode is Windows on all web sites.
The <authorization> node in particular is identical between web sites.  
The local domain is the same MS Windows Server 2008 virtual machine in all cases -- one server image hosting multiple web sites. So in theory, user authorizations should be identical across all web sites.
--Edit 1-- Just my luck. I had this authorization issue pop up on web site 1, on a JavaScript file that has run just fine before, during a sprint review. There was the twist that in this case, the user was able to go through quite a few pages before the authorization failed.
I'll post my logs as soon as I can.
--Edit 2-- I did make one environment change shortly before this issue started: I updated jQuery and Bootstrap.
Here's my diffs in packages.config:
Before
  <package id="AspNet.ScriptManager.bootstrap" version="3.3.5" targetFramework="net45" />
  <package id="AspNet.ScriptManager.jQuery" version="2.1.4" targetFramework="net45" />
  <package id="bootstrap" version="3.3.5" targetFramework="net45" />
  <package id="jQuery" version="2.1.4" targetFramework="net45" />
After
  <package id="AspNet.ScriptManager.bootstrap" version="3.3.6" targetFramework="net45" />
  <package id="AspNet.ScriptManager.jQuery" version="2.2.3" targetFramework="net45" />
  <package id="bootstrap" version="3.3.6" targetFramework="net45" />
  <package id="jQuery" version="2.2.3" targetFramework="net45" />
And here are two typical entries in the Application event log, appropriately sanitized.
1:
Event code: 4008 
Event message: File authorization failed for the request. 
Event time: 6/2/2016 2:31:29 PM 
Event time (UTC): 6/2/2016 6:31:29 PM 
Event ID: e4a0fd65d9e34686967f14429d21ab97 
Event sequence: 14 
Event occurrence: 1 
Event detail code: 0 
Application information: 
    Application domain: /LM/W3SVC/21/ROOT-1-131093658656731243 
    Trust level: Full 
    Application Virtual Path: / 
    Application Path: C:\Users\Administrator\Documents\Visual Studio 2013\Projects\HAWK_WebForms\HAWK.Web.LogansRun\ 
    Machine name: BAH01 
Process information: 
    Process ID: 5288 
    Process name: iisexpress.exe 
    Account name: HAWK\administrator 
Request information: 
    Request URL: http://localhost:53104/Scripts/jquery-2.2.3.js 
    Request path: /Scripts/jquery-2.2.3.js 
    User host address: ::1 
    User: HAT\john.smith
    Is authenticated: True 
    Authentication Type: NTLM 
    Thread account name: HAWK\administrator 
Custom event details: 
2:
Event code: 4008 
Event message: File authorization failed for the request. 
Event time: 6/2/2016 2:28:51 PM 
Event time (UTC): 6/2/2016 6:28:51 PM 
Event ID: a43d7292a8894df193600e829e74c696 
Event sequence: 14 
Event occurrence: 1 
Event detail code: 0 
Application information: 
    Application domain: /LM/W3SVC/14/ROOT-1-131093657141125131 
    Trust level: Full 
    Application Virtual Path: / 
    Application Path: C:\Users\Administrator\Documents\Visual Studio 2013\Projects\HAWK_WebForms\HAWK.Web.LogansRun\ 
    Machine name: BAH01 
Process information: 
    Process ID: 5248 
    Process name: iisexpress.exe 
    Account name: HAWK\administrator 
Request information: 
    Request URL: http://localhost:53752/Scripts/Pages/Admin/SelfRatingWizard.js 
    Request path: /Scripts/Pages/Admin/SelfRatingWizard.js 
    User host address: ::1 
    User: HAWK\james.jones
    Is authenticated: True 
    Authentication Type: NTLM 
    Thread account name: HAWK\administrator 
Custom event details: 
--Edit 3--
I tried adding the registry key from this answer: https://stackoverflow.com/a/13015279/2615836
It didn't change anything. I also double checked the order of the authentication providers. NTLM is already ahead of Negotiate for all the sites.
--another update--
I rolled back Bootstrap and jQuery.  To my astonishment, the file authorization still fails!  Again, jQuery.js is one spot -- just about every file raises this complaint.  It's as if the authorization token gets "forgotten".
--update to Edit 1--
The JavaScript file that was raising issues in web site 1 did not have permissions for Network Service like all the other JavaScript files did.  Once I fixed that, web site 1 was resolved.  Alas, this fix did not resolve web site 2.
 
     
    