I've been using x264vfw + VDub to make Youtube vids. I usually set threads to "0" for my quad core. It has worked fine like that for many videos. However, very recently this causes the processing to fail on Youtube. I narrowed it down to the threads setting by uploading many small test videos (varying individual settings among them).
I noted too that the file size between encodes with a threads setting of 1 (default) have a different file size than those with a different threads setting.