Quando você abre um terminal a partir de sua área de trabalho, o terminal herda o ambiente em que foi iniciado, incluindo o PATH. Quando você abre um terminal, o seguinte acontece de acordo com a documentação do Bash:
Do Manual de referência do bash
When Bash is invoked as an interactive login shell, or as a non-interactive shell with the --login option, it first reads and executes commands from the file /etc/profile, if that file exists. After reading that file, it looks for ~/.bash_profile, ~/.bash_login, and ~/.profile, in that order, and reads and executes commands from the first one that exists and is readable. The --noprofile option may be used when the shell is started to inhibit this behavior.
When a login shell exits, Bash reads and executes commands from the file ~/.bash_logout, if it exists.
E ...
When an interactive shell that is not a login shell is started, Bash reads and executes commands from ~/.bashrc, if that file exists. This may be inhibited by using the --norc option. The --rcfile file option will force Bash to read and execute commands from file instead of ~/.bashrc.
So, typically, your ~/.bash_profile contains the line
if [ -f ~/.bashrc ]; then . ~/.bashrc; fi
after (or before) any login-specific initializations.
Portanto, para que o seu .bash_profile seja executado, você precisa fazer o login em um shell de login, talvez fazendo o ssh no host local, ou fazendo logout do seu ambiente de desktop e logando novamente.