heres what i did:
goto ispconfig uncheck ssl and delete the certificates... click save..
now wait a few minutes or just run the cron urself.
now edit ispconfig settings:
# vi /usr/local/ispconfig/server/plugins-available/apache2_plugin.inc.php
goto line 140 and change 1024 to 2048 or 4096.
run the cron again, u should see ispconfig generate new keys.
at this step i reloaded apache..
go back into ispconfig, click create certificate and enable ssl.
run the cron, u should see ispconfig creating the keys now...
reload apache, relogin in ispconfig.. your certs should be there now.
now u can use your ssl request file and let it sign from whereever u get your certificate.. replace the certificate created by ispconfig with your signed one.
at this step it worked for me.. also i followed another tutorial so i added 2 more files and pasted the following lines into the options / apache directives form.