I have no explanation why turning on/off of logging would fix a Couatl crash. However, a Couatl crash CANNOT cause a crash of the sim, since Couatl, being an external .EXE, doesn't have the means to affect the sim stability.
But, if you have the antivirus enabled, and you haven't added ALL your scenery folders to the antivirus exclusion list, it's possible the antivirus itself (the antivirus, being a Windows service CAN crash any app), as soon as it saw Couatl scanning for all the scenery files, started to scan each file opened by it, and this would cause both a huge slowdown, and in some cases a crash of the sim, especially if a corrupted or a zero-lenght size .BGL is found.
So, add all your scenery folders (and the main simulator root folder too), to the list of the antivirus exclusions. This would made the cache rebuild process faster and less likely to cause problems when finding corrupted files.
And, you don't have to *always* restart and rebuild the scenery cache.
The only time you must do that, is when you RENAME or DELETE an AFCAD. Some sceneries that come with "switchers" between multiple AFCAD will do a rename and, since GSX doesn't check *all* files (it would be very slow if it tried to do that, since you might have ten of thousands of them), but only checks the folder last modification date, when a single .BGL inside a folder is removed or renamed, the folder last modification date doesn't change, so GSX cannot detect a change and you need to "Restart and rebuild cache".
Here's a post that suggest a way to automatically have the cache rebuilt after running the FlyTampa configurator:
http://www.fsdreamteam.com/forum/index.php/topic,17222.msg121251.html#msg121251