OK, this is a bug then.
I found the problem. It seems like ISPC _does_ save the file into the new www.sitename.com.crt
file under /ssl/, though it does not restart apache.
I manually had to HUP apache and it refreshed it's certificates and loaded the new cert, then it worked fine.
I am running ISPC 2.2.12
Or is this fixed in the new version?