I did some additional testing this evening with vanilla setup of Owncloud 6.0.2 + PHP 5.3.x on Ubuntu 12.04 LTS box. Unfortunately that didn't help either. It seemed that this setup didn't get as far as the previous one. To counter lack of real certificate on this setup I also tested with plain http.

Earlier tested setup was Owncloud 6.0.3 + PHP 5.4.x + RHEL6 + proper certificate. With that I had today couple of hours session checking through configurations for possibly conflicting modules, php packages, web server hardening config and virtual directory request commands. Basically anything I was able to found about owncloud webdav problems. None had any effect, and CargoDock still bombed after 405 error.

Server side error and access apache logs showed only one request for PROPFIND verb, which gave out 405. I suspect this is not the reason, as working clients do have these too, and it may be connected to unrelated file locking problems with owncloud.