Yutaka,
I've double checked the "Close on Exit" option - it's unchecked.
When the running script (configured via EmEditor External Tools) exits, the Output Panel remains open, but all it's STDOUT strings disappear from the Output Panel.
If I put `pause` in the end of the script, it remains in the memory and its STDOUT strings present i the EmEditor Output Panel until exit of the script.
I'm using the v11.0.0 of the EmEditor on the windows 7 64-bit machine.