Why does it take so long for Handbrake to finish the encoding process?

I have a Core i7 q820 and I can convert my 650 MB video files from H.264 to MP4 in about 10 minutes.. but right at 99%, it stops and takes another 30 minutes to finish! I don't have this problem when converting to any other format. What the heck is taking so long? Is it some sort of bug?