Difficult to say on this one. I'm not an ISPConfig expert (I've only been using it since August last year), but I wonder if it's the lack of a CSR that could be causing the problem.
Now you don't actually need the CSR in order for the web server to start - that just reads the key and the cert (from separate files such as /var/www/web1/ssl/www.mysite.com.key etc), but I just wonder if perhaps this is causing problems with ISPConfig rather than apache.
What you could do is put the correct .key and .cert files in the relevant directory manually again, don't touch ISPConfig, and restart apache (eg. apachectl restart or /etc/init.d/httpd restart etc).
In fact, if you do apachectl configtest first, that should tell you if the key/cert is valid. You can then test the site again in a browser (close it and re-open just to be sure) to see if it's the right cert. If it is, then you can test again putting the CSR and the Cert into the site's SSL tab in ISPConfig. I've done this successfully, but then again I did have the original CSR used to generate the certificate. I would have thought you might struggle without that.
With this sort of problem, you usually find the solution by careful step-by-step analysis of what's actually going on, and careful reasoning. (aka trial and error!)
Hope you get it sorted. Feel free to post back - not sure I could be any more help though...