I am using v18.104.22.168 as I find later versions much slower at transcoding.
Check if the problem is related to a particular file or not. If it is, you may be able to 'fix' the file by 'converting' it. I have found converting from an AVI to an AVI can sort things out. Google for something that suits you. Also, setting NVE to high priority and waiting (usually a few minutes does it here) does the trick.