This issue seem to have been addressed in RouterOS version 6.43, so it is much easier to fix these issues now.
http://forum.mikrotik.com/t/v6-43-current-is-released/123160/1
So something like this should work to fix your netwatch scripts.
/system script
set [find name="Netwatch up script"] dont-require-permissions=yes
More information can be found on the new Scripting_Tips_and_Tricks manual page.
here: https://wiki.mikrotik.com/wiki/Manual:Scripting_Tips_and_Tricks#Check_script_permissions
Sadly it is not included in the v6.42.12 long-term. So upgrading from v6.40.9 long-term to v6.42.x will still break all netwatch script.