The system.log is being filled with these messages. It doesn't stop.
Mar 11 14:18:41 com.apple.xpc.launchd (com.dejal.timeout.launcher): Could not find and/or execute program specified by service: 155: Refusing to execute/trust quarantined program/file: com.dejal.timeout.launcher
I already reinstalled from the Web site to no avail.
The following command did not help:
xattr -d -r -s com.apple.quarantine /Applications/Time\ Out.app
Then I tried the same on ˜/Library/Application Scripts/com.dejal.timeout.launcher
This did not help either.
The following message might be an unrelated Sierra bug?
Mar 11 14:18:41 com.apple.xpc.launchd (com.dejal.timeout.launcher): Service only ran for 0 seconds. Pushing respawn out by 10 seconds.
(The post at http://dejal.com/forums/2016/01/26/time-out-not-showing-overlay did not help to resolve this, just to be clear, and the overlay is showing)
Hope you can help.