Servers with PHP as FCGID stopped working after update to 0.96

Please have a look at my question there:
https://www.virtualmin.com/node/24245

Since I updated to 0.96, clients were directly served the content of the PHP file, except under SSL, where it was still working. I had to manually change every server to use mod_php, which will bring ownership problems.

Here is the content of an untouched Apache config file after update:

<VirtualHost 37.59.44.173:80>
SuexecUserGroup "#1014" "#1007"
ServerName app.domain.com
ServerAlias www.app.domain.com
DocumentRoot /home/nababx/domains/app.domain.com/public_html
ErrorLog /var/log/virtualmin/app.domain.com_error_log
CustomLog /var/log/virtualmin/app.domain.com_access_log combined
ScriptAlias /cgi-bin/ /home/nababx/domains/app.domain.com/cgi-bin/
DirectoryIndex index.html index.htm index.php index.php4 index.php5
<Directory /home/nababx/domains/app.domain.com/public_html>
Options -Indexes +IncludesNOEXEC +FollowSymLinks +ExecCGI
allow from all
AllowOverride All
AddHandler fcgid-script .php
AddHandler fcgid-script .php5
FCGIWrapper /home/nababx/domains/app.domain.com/fcgi-bin/php5.fcgi .php
FCGIWrapper /home/nababx/domains/app.domain.com/fcgi-bin/php5.fcgi .php5
</Directory>
<Directory /home/nababx/domains/app.domain.com/cgi-bin>
allow from all
</Directory>
Redirect /stats http://app.domain.com/cgi-bin/awstats.pl
RemoveHandler .php
RemoveHandler .php5
IPCCommTimeout 31
Alias /pipermail /var/lib/mailman/archives/public
FcgidMaxRequestLen 1073741824
php_admin_value engine Off
</VirtualHost>
<VirtualHost 37.59.44.173:443>
SuexecUserGroup "#1014" "#1007"
ServerName app.domain.com
ServerAlias www.app.domain.com
DocumentRoot /home/nababx/domains/app.domain.com/public_html
ErrorLog /var/log/virtualmin/app.domain.com_error_log
CustomLog /var/log/virtualmin/app.domain.com_access_log combined
ScriptAlias /cgi-bin/ /home/nababx/domains/app.domain.com/cgi-bin/
DirectoryIndex index.html index.htm index.php index.php4 index.php5
<Directory /home/nababx/domains/app.domain.com/public_html>
Options -Indexes +IncludesNOEXEC +FollowSymLinks +ExecCGI
allow from all
AllowOverride All
AddHandler fcgid-script .php
AddHandler fcgid-script .php5
FCGIWrapper /home/nababx/domains/app.domain.com/fcgi-bin/php5.fcgi .php
FCGIWrapper /home/nababx/domains/app.domain.com/fcgi-bin/php5.fcgi .php5
</Directory>
<Directory /home/nababx/domains/app.domain.com/cgi-bin>
allow from all
</Directory>
Redirect /stats http://app.domain.com/cgi-bin/awstats.pl
RemoveHandler .php
RemoveHandler .php5
IPCCommTimeout 31
Alias /pipermail /var/lib/mailman/archives/public
FcgidMaxRequestLen 1073741824
SSLEngine on
SSLCertificateFile /home/nababx/domains/app.domain.com/ssl.cert
SSLCertificateKeyFile /home/nababx/domains/app.domain.com/ssl.key
</VirtualHost>