Just to make sure if someone else comes across this the proper way to do this is following:
1) If applicable make sure you first remove both preconfigured makemkv-bin makemkv-oss directories if you are installing same version, in other words delete preconfigured then uncompress new directories to configure
> Step 1 is very important, if installing same version and if you omit it and follow steps below you will NOT compile with necessary libraries to see TrueHD
2) I choose to follow uninstall instructions here
>
http://www.makemkv.com/forum2/viewtopic.php?f=3&t=3924
# Remove the config files
rm -fr ~/.MakeMKV
# Remove the actual program
sudo rm /usr/bin/makemkv
sudo rm /usr/bin/makemkvcon
> Not sure if 100% necessary but these are my steps
3) Follow the install guide here for Linux
>
http://www.makemkv.com/forum2/viewtopic.php?f=3&t=224
> First do this part OPTIONAL: Building with latest libavcodec.
> I chose the 2nd configure option
> ./configure --prefix=/tmp/ffmpeg --enable-static --disable-shared --enable-pic --disable-yasm --enable-libfdk-aac
> If you get an error saying something like > libfdk_aac not found then do following:
sudo apt-get install libfdk-aac0 libfdk-aac1 libfdk-aac-dev
> I found I needed all three for it to work
4) Build makemkv-oss under the OPTIONAL section
5) Build makemkv-bin as normal
If configured correctly you will have to accept makemkv license agreement. You may have to reenter your registration code.
Hope this helps.