The most common reason for this is that one of your scripts has an incorrect number of { or } and this is causing the /set command to be overridden. To track it down, you would need to unload your scripts one at a time, use the /set command in the status window and then check the variables section. If the variable is set as expected, you have narrowed the issue down to a particular script. You would then need to load the script and check the aliases defined in it to narrow the cause of the issue.
