Drupal multi site 404s, sub directory site subpages going to default site We have a strange set of errors going on with a dev (and stage) version of our drupal multisite.
We have some sub directory sites, and some sites server up on different urls. One URL is an internal one to the Host. The other is an external one (that goes through a firewall).

The essence of the problem is this


the sub directory site homepage displays fine, but any sub pages you click through to come up as 404s -- the 404 that is thrown is on the default site. This happens with sub directory sites on both URLs (external and internal). 
I am unable to access site pages using index.php?q=
Some pages that get served up properly, are still showing up as a 404. This doesn't seem consistent on all sites, but it seems weird to begin with.


What I know


The .htaccess is being used by the sites 
ModRewrite is on.
At our request, the ISP put some restrictions on one of the URLs.
The same structure works fine on our production site (minus the restricted URL)
sites.php is working fine, so far as I can tell.


What are the things that we could still have configured wrong (our hosting company is equally perplexed)? The problem seems to coincide with locking down the internal URL (to be only visible to VPN).

For now, I can share this URL: http://contentdev.sierraclub.org/coal
Click on a sub link.
Compare to http://content.sierraclub.org/coal

Any ideas would be very much appreciated.
You didn't mention anything about sites.php, so I'm going to guess that's where the problem resides.

Google it: https://www.google.com/#q=drupal+multisite+sites.php 
D7 example: https://api.drupal.org/api/drupal/sites!example.sites.php/7.x 
D8 example: https://api.drupal.org/api/drupal/sites!example.sites.php/8.2.x

Please post your sites.php file if you're unable to fix the issue after taking a look.