Just followed your advice, enabled apps and then done the wipe partition and rebooted but still no joy?
Then re-traced what you did before, how you disabled the Weather widget? Maybe you uninstalled one of the apps instead of just disable it. If you don't recal uninstalling apps then go to the Application manager and look for all apps related to Weather (I think they are Weather and Weather daemon, but maybe others) and clear cache and data on all of them. Try again.
If still nothing, then in order to avoid a Full factory reset (If you are willing to do so just for the weather widget remember that you can always try the Xwidget app with the Weather widget I posted some time ago) then go to application manager and look for Touchwiz home, if you clear cache and data of it I'm almost sure that it will reset all your Touchwiz settings, not your data, but I think that after you re-arrange everything the way you have it now, it may fix your issue.
Last option, factory reset, but like I mentioned above, I'd try using Xwidget, I'm using it, since I'm using Nova Launcher and the weather widget is not available for other launchers, and it looks just like the original one. Try this thread and even when the original file I upload is not available now for some strange reason, Xwidget has already the S6 Weather widgets, so you just download from them and use it.
http://forums.androidcentral.com/samsung-galaxy-s6/529230-alternative-original-weather-widget-third-party-launchers.html