I would like to open them in konqueror.
You are using the xine plugin
with conqueror to play multimedia?
Have you tried dragging the file to the konqueror window?
Have you set konqueror to open new instances (of anything) in an existing window?
The strange color thing happens with different file types, wmv, mpeg but not all of them, it seems to be random.
Random? In that sometimes foo.mpg is distorted and sometimes it ain't? Or that it isn't associated with file formats that you play?
You are likely seeing the effect of DRM-encumbered files. wmv, avi, and mpeg-4 files are designed to break like this. (Amongst others.)
Have you seen the distortion an any free formats?
Have you checked the distorted files for DRM?