I am really sorry for not responding for over a month now. Your replies somehow slipped my awareness and I had already arranged myself with not beeing able to sync the contacts from threema. However today this bugged me again and I tried a different app (CardDAV Sync from playstore) for syncing my owncloud contacts. And voilá, syncing worked with that one. So I actually came back here to report this as I figured it might help to figure out which end is faulty here. But now I see you seem to already have looked deeply in to my problem, even installed Threema yourself. Thank you for your support! And again, sorry I didn’t reply here…
Anyway, my mails with Threema support are all in German, so I’ll try to sum up what I’ve learned:
Threema creates a new account with its own address book in android upon installation. It stores the threema ID of each contact that was previously matched in a field “sync1” within this Threema address book.
But since you report that it just works I will now try and remove all addressbooks as well as Threema and start from scratch. Maybe this helps. This time I’ll report back!