I have a repo to which I connect via https. The problem is that it uses a self-signed certificate and I to tell svn each time to trust the certificate (even so that I tell it to accept it permanently).
I suggest you try to checkout the repo from SVN trough command line for the first time. SVN should catch-up that the certificate is untrusted and ask whether you want to accept it permanently. I believe from then on you can proceed with Subversion bundle and your certificate without any problem, as AFAIK this bundle calls "svn" command internally anyway.
I've also self-signed certificate and I used command line to accept the certificate once permanently and now everything works smooth.
Cheers,