I have experienced this problem before and the only way I managed to resolve it was by deleting the complete mainmenu section and re installing that whole section.
What happens is that the green arrows are missing when i create a new sub menu item. This then leads to a problem of reordering that item.
My website is growing all the time and this is becoming a headache to say the least!
Are you able to reorder them by changing the numbers in the box, ie Charities > 2 and Churches > 1 and then clicking the little icon (save order) at the top of that column?
Have you tried moving part of the offending section (say, Charities) out into the root of the menu and back in to see if it auto-magically sets the correct values again? Only a little less painful than deleting it, I know.
However, when I placed it under "Top" those little green arrows reappeared but when I moved it back they were nowhere to be seen. Strange or what!
I really think it would be a good idea if a Joomla expert could look into this to see what is going on as surly I am not the only one to have this problem? If there is anyone out there that would like to take a look behind the programme on my website I would be happy to hear from them. This may well turn out to be a bug in Joomla that needs attention.
Actually, I have the same issue with the same template. I've tried the suggestions above but no joy (but in my case, it's not a big problem). I'd try another template to see if the problem persists but I just went live yesterday (sorry).