Have to highlight to see Terminal color

What is your OS, Pycharm version? Could you please attach a screenshot with Settings(Preferences fo OS X)| Tools| Terminal?

Ubuntu 16.04.2 LTS

PyCharm Community Edition 2017.2
Build #PC-172.3317.103, built on July 25, 2017
JRE: 1.8.0_152-release-915-b5 amd64
JVM: OpenJDK 64-Bit Server VM by JetBrains s.r.o
Linux 4.10.0-28-generic

Does it help if you change Console background color in "Settings| Editor| Color Scheme| Console Colors| Console| Background"?

Nope, I also tried changing it to black.   I guess the issue is that pycharm terminal is applying some setting of its own so that it displayed something different than gnome-terminal.  The other possibility I can think of is that terminal is not compatible /w tmux. 

Ok so the only color theme that display properly with terminal was Github scheme which has a bright setting.  I think perhaps a better setting is to not have the IDE scheme apply to the terminal window if possible.

I manged to resolve this awhile ago; the issue was actually due to running tmux.  My solution is to add to my .zshrc (or .bashrc) to detect if the terminal is launched by Intellij (which show java type) and only launch tmux if it is not java type:

local TERMINAL=$(ps -p$PPID | sed '1d' | awk '{print $4}')

if [[ $TERMINAL != "java" && "$TMUX" != "screen-256color" ]]; then
 echo "start tmux ..."
 tmux
fi

Hope this can help someone. :)