Ok - I did some testing and found the reason which causes this behavior (but I don't know where & when this happens):
When a new maildomain is created and the spamfilter is not activated (during maildomain creation) it causes the described behavior. E.g. all newly created mailboxes are owned by the wrong user.
If the spamfilter is activated, the maildomain-directory has the owner "vmail" permission-set 0700 (and not 0755 - which happens when the spamfilter is not activated) and all mailboxes are created within this domain have the correct owner.