SetHandler seems to be ignored - apache

Question

Installing shibboleth on apache 2 on Ubuntu 14.04LTS. Actual shib install seems to go fine, so configure the site .conf file to use shibboleth.
When I access https://lib.msu.edu/secure, it is handled by shibboleth (with an appropriate config exception at this stage), but when I access https://lib.msu.edu/Shibboleth.sso/Metadata (or anything else in Shibboleth.sso) it get redirected to php/drupal and never seen by the shibboleth system and gets a 404 error.
My best guess is that apache is not passing the request to shibboleth, but I am not sure why, nor how to debug the situation. This all worked fine on our test server and we cannot find any configuration differences that explain why.
apache .conf file follows:
<VirtualHost *:443>
ServerAdmin webmaster#localhost
ServerName lib.msu.edu
ServerAlias library.msu.edu
ServerAlias [...]
DocumentRoot [MyValidRoot]
<Directory [MyValidRoot]>
Options Indexes FollowSymLinks MultiViews
AllowOverride All
Order allow,deny
allow from all
</Directory>
<Location /Shibboleth.sso>
SetHandler shib
</Location>
<Location /secure>
AuthType shibboleth
ShibRequireSession On
Require valid-user
</Location>
SSLEngine on
SSLCertificateFile [validcertpath]
SSLCertificateKeyFile [validkeypath]
SSLCertificateChainFile [validIntermediateCertpath]
SSLProtocol all -SSLv2 -SSLv3 -TLSv1
SSLCipherSuite [cipherString]
SSLHonorCipherOrder on
SSLCompression off
SSLUseStapling on
SSLStaplingResponderTimeout 5
SSLStaplingReturnResponderErrors off
Redirect /cgi-bin/ [CGIserver]/cgi-bin/
# Redirect all requests to lib.msu.edu (except wwwm, for testing mirror)
<If "! req('Host') in { 'lib.msu.edu', 'wwwm.lib.msu.edu' }">
Redirect / https://lib.msu.edu/
</If>
RewriteEngine On
# force trailing slash
RewriteCond %{REQUEST_METHOD} !=post [NC]
RewriteRule ^(.*(?:^|/)[^/\.]+)$ $1/ [L,R=301]
# redirect .js and .css 404s to tomcat
RewriteCond %{REQUEST_URI} \.(css|js)$
RewriteCond /var/www/mainweb%{REQUEST_URI} !-f
RewriteRule ^/(.*)$ https://tomcat.lib.msu.edu/$1 [L]
</VirtualHost>
Thank you for any help you can give! We have already spent hours banging our heads on this shibboleth install.