Solving this problem took two steps:
Add this to your .bashrc / .bash_profile / .zshrc:
# load virtualenvwrapper for python (after custom PATHs)
venvwrap="virtualenvwrapper.sh"
/usr/bin/which -s $venvwrap
if [ $? -eq 0 ]; then
venvwrap=`/usr/bin/which $venvwrap`
source $venvwrap
fi
Then use:
source .bash_profile
# or .bashrc / .zshrc
to reflect the changes.
Additionally, if the terminal still sometimes cant find workon, use source .bash_profile to reset and find it again.