Dang it. That's on me. When I was adding that setting, I changed the name that is used in the game's config file at one point. Since my dev file had both the old and new name in it, i thought it was working correctly. But what's happening is that it uses the old property name to read the setting, and the new property name to save the setting.
It's easy to fix though. In a text editor (WinAGI has a text editor built in!), open up your winagi.config file, which can be found in your install directory, usually in 'Program Files (x86)\WinAGI GDS'. If it's not there, try 'Users\{user}\AppData\Local\VirtualStore\Program Files\WinAGI GDS'*** - Windows 10 sometimes moves program configuration files automatically.
Find the [Decompiler] section, and add this line:
MsgsByNum = True
then save the file. If the line is already there, just change the value to 'True'. Ignore the line that says 'MsgsByNumber = True'. If you want to change the setting later, you'll have to manually edit the config file again.
I'll get a fix out that addresses this permanently by the end of the week.
Sorry for the inconvenience.
***The AppData folder is a hidden folder; if you don't see it, make sure you configure File Explorer to show hidden files and folders.