From reading some of the other support reports, it sounds like Sync can cause unexpected behavior with NoScript's whitelist. If I understand it correctly, NoScript's whitelist and other preferences are automatically modified by Sync if "Preferences" is selected in Sync. I see that there is an about:config pref, noscript.sync.enabled, with a default value of true.
I have a couple of suggestions.
1) Expose the pref in the UI.
2) Set it to false by default.
Even if the Sync issues are eventually resolved, NoScript would be easier to support if false were the default value. Part of the current troubleshooting routine is for the user to reset NoScript. The problem is that if Sync is enabled by default, then the user's settings may be changed to an unknown state by Sync while troubleshooting. Sounds like troubleshooting hell to me.