Hi
Okay, luckily, because i discovered (as you have) it was a template issue, I contacted Gavick, who supply any templates I use, and their support was able to pinpoint the problem, which was a library being added by an extension (in my case Smart Search). So its the template in combination with a particular extension that is causing this issue.
The likelihood is that you have different extensions installed between the two sites you mentioned, and maybe you could start there, by looking at what the differences are? In any case, you will find the problem if you disable all your extensions in turn and check as you go. Quote from Gavick support is below.
"Please disable all extensions and than start publishing them one ofter the other while checking the dropdown. One of this extensions is adding chosen library which has to be disabled."
Good luck