The crt, scr etc are your certificate, signing request and key files, so they're all there. You can check the /etc/apache2/vhosts/vhosts_ispconfig.conf file as well.
That'll have a section for your website that starts
<VirtualHost ip.ad.dr.ess:443>
ServerName
www.yourdomain.com:443
and a bit further down should be
SSLEngine on
SSLCertificateFile /var/www/webXX/ssl/www.yourdomain.com.crt
SSLCertificateKeyFile /var/www/webXX/ssl/www.yourdomain.com.key
listing the files you just mentioned.
If you were using suPHP you would have consciously installed it, If Suexec is installed I think it gives you an enable 'tickbox' in the ISPConfig website setup.
A drastic check is to enter
a2dismod suexec
If it was enabled, that will disable it, an error message means it wasn't.
a2enmod suexec
would re-enable.
After all the to and froing with the certificates, it's probably a good idea to restart the web server explicitly as well.
/etc/init.d/apache2 restart
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