I just solved the problem myself.
i am running multiple subdomains on the same ip address with ssl encryption. i redirect my incoming requests to subfolders of my wwwroot using mod_rewrite and based on the used domain names. this works of course only if every request sent to the server contains the FQDN. it seems that FolderSync does not send the FQDN on every request while ES-File Explorer does.
in order to fix that i created a link in the default directory where all unmatched requests would end up so that it will find owncloud again. has anyone tested this sort of behaviour with multiple virtual hosts using ssl on a single ip address? i suspect that you might have the same issue because apache would also need the domain name to distinguish which virtualhost the request belongs to.
so for anybody interested in a solution here is how i am doing it now:
DocumentRoot of my owncloud installation: /var/www/owncloud
DocumentRoot of my default virtual host: /var/www/pub
URL of owncloud:
https://owncloud.mydomain.com/i then created a symlink in the default DocumentRoot to link to the owncloud root:
# ln -s /var/www/owncloud /var/www/pub/owncloud
and a symlink within owncloud back to itself, so that even with the correct http header it will reach itself through the same url:
# ln -s /var/www/ownlcoud /var/www/owncloud/owncloud
now i simply use
https://owncloud.mydomain.com/owncloud(/remote.php/webdav) as my server's url and it all works :)
hope this helps someone some day
regards
Pascal