What probably happened is LE made its default conf and it's loading it before the seedbox confs causing it to conflict.
A bit of editing is required. Grab the certificate locations from the file
/etc/apache2/sites-enabled/000-le-default.conf (or similar). This is likely something to the effect of:
and paste/overwrite the values for the same lines in the file
Remove 000-le-default.conf and reload the apache config with
service apache2 reload. Everything should be working after this
Edit: I suppose the sed command should fix things as well