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
and a bit further down should be
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
If it was enabled, that will disable it, an error message means it wasn't.
After all the to and froing with the certificates, it's probably a good idea to restart the web server explicitly as well.