3 hours to convert a 30 minute tv show?

So after reinstalling MceBuddy my conversions are super slow, I have it set to Normal, convert to MP4 Normal. IT will start and say moving to working directory, sits and does nothing for at least 30 minutes, when it finally starts it say pass 2 and shows an estimated time of lets say 6 minutes 10 seconds, then the timer freezes but the percentage goes up a little, when the timer starts again it says estimated time 6 minutes 53 seconds- so it paused for like a full 60 second minute and when it restarted the timer went up instead of down, this continues back and forth for about 30 minutes, when it finally finishes it now says removing commercials, that goes pretty quick.
Now when it starts to what I hope is the final step it says 2 hours 53 minutes.
I know, you want to see the logs, I will need to wait for this one to finish, if it does it will be after I’m asleep but I will attach the logs tomorrow.

I assume you are not using hardware acceleration , what are your system stats. It may just be you don’t have enough horsepower to do software encoding in a timely fashion. I’m confused as to why you have 2 passes but say you have it set to normal quality which is only one pass but still slow if you have an older system. Before I started using a good video card and did software encoding set to normal it would take my system 4 hours to do the average movie with one pass and no commercial removal. My machine is only a i5 4690K with 8 gigs of RAM.