Alright, so this is what is wrong:

cd ~/steem/programs/steemd/witness_node_data_dir 
wget http://steemitup.eu/witness_node_data_dir.tar.gz && tar xvzf witness_node_data_dir.tar.gz

The TAR file contains a directory named witness_node_data_dir so when it's extracted it placed here:

cd ~/steem/programs/steemd/witness_node_data_dir/witness_node_data_dir 

So to fix this just run:

cd ~/steem/programs/steemd/
wget http://steemitup.eu/witness_node_data_dir.tar.gz && tar xvzf witness_node_data_dir.tar.gz

Then download and extract the blockchain:

wget http://steemitup.eu/witness_node_data_dir.tar.gz && tar xvzf witness_node_data_dir.tar.gz

I think that's the only thing I did different besides VirtualBox.