I need to convert a ton of files over to the correct format to play on my Dish Hopper/Joey.

Converting using KooRaRoo us much easier because it seems to have all of the inner workings of FFMPEG figured out and makes a perfect file when output.

Here's a sample of code that's used when FFMPEG is executed via KooRaRoo (grabbed from ProcessExplorer).

"C:\Program Files\KooRaRoo Media\ffmpeg.exe"  -i "\\DISKSTATION\storage\movies\m4v\Escape from Planet  Earth (2013, Rated PG) (2013, Rated Unknown).m4v"   -y  -c:v libx264  -b:v 1312837 -bt 131283  -r 23.98  -level 51  -profile:v high -filter:v "yadif, format=yuv420p, scale='(gte(trunc((iw*1080)/ih), 1920) * 1920 + not(gte(trunc((iw*1080)/ih),1920)) * trunc((iw*1080)/ih)) : gte(trunc((iw*1080)/ih),1920) * trunc((ih*1920)/iw) + not(gte(trunc((iw*1080)/ih),1920)) * 1080', pad='1920:1080:(ow-iw)/2:(oh-ih)/2', scale='(gte(trunc((iw*720)/ih), 1280) * 1280 + not(gte(trunc((iw*720)/ih),1280)) * trunc((iw*720)/ih)) : gte(trunc((iw*720)/ih),1280) * trunc((ih*1280)/iw) + not(gte(trunc((iw*720)/ih),1280)) * 720', pad='1280:720:(ow-iw)/2:(oh-ih)/2', setdar=16/9"  -map 0:0   -c:a ac3_fixed  -b:a 448000  -ar 48000  -ac 6  -map 0:2  -dn -f matroska   -threads 0 -crf 23 -preset superfast -map_metadata -1 "F:\KooRaRoo Transcoding\KooRaRoo_Transcoding\matroska_h264_level51high_00_ac3_02_11\124-41.krrv"
I noticed that when I convert files using KooRaaRoo, the conversion/transcode is very slow. When I look at CPU usage, it's very low as well (14% in the screenshot below), I have all sorts of CPU left over (this is one powerful box).

Before you mention that it's converting files from a network location. The files transcode at the exact same speed when moved over to the local hard drive, so the network doesn't seem to be the bottleneck.

How can I fix this beyond calling FFMPEG externally and somehow trying to mimic the command triggers that KooRaRoo is using?

Any ideas? This is going to take forever at this rate.