Since this seems due to a currently unfixed bug in Spring I added a workaround using POST and a different path so it does not confilct with my other POST-Mappings.

Code:
	/* Usually you would use a mapping to HTTP-PUT in a REST-Application.
	*Since there is a BUG with multipart-requests and HiddenHttpMethodFilter
	*we use a different path and the POST-Method here
	*https://jira.springsource.org/browse/SPR-6594
	*/
	@RequestMapping(value="/scriptfile/{id}/update", method = RequestMethod.POST)    
    public String update(@Valid ScriptFile scriptFile,
    							BindingResult result,
    							ModelMap modelMap, HttpServletRequest request) {    
        if (scriptFile == null) throw new IllegalArgumentException("A scriptFile is required");        
        if (result.hasErrors()) {        
            modelMap.addAttribute("scriptFile", scriptFile);            
            modelMap.addAttribute("showcases", ShowCase.findAllShowCases());            
            return "scriptfile/update";            
        }
        setFileParameters(scriptFile, request);
        scriptFile.merge();        
        return "redirect:/scriptfile/" + scriptFile.getId();        
    }