Unfortunately it will be hard to debug or help here from remote. You most likely need to work your way through the already known resources at [1] and [2].
As an alternative just wait for the upcoming ownCloud 10.0 which uses WebDAV PUT for WebGUI uploads which mostly works around environmental (webserver config, php) issues which are most likely the reason for such issues like seen here.
[1] ownCloud Documentation Overview
[2]