We breed mainly Toggenburgs (though we've only got/had Boers, Angoras, Saanens, Anglo Nubians, Australian Browns and more) and I've actually never had a problem with them being 'independant' any more than other breeds - a wild Togg and a wild Saanen are (the ones I have seen at least) the same thing. However, it does tend to rely on the raising, as some Togg kids are definitely more stubborn than the average kid (I have a line here where it is inherited to be stubborn), but there is still a great variation within every breed from what I have found andour Toggs are normally no more independant than other breeds. (the most independant goat we ever had, although she was extremely friendly as well, was a Saanen, and the wildest was probably an Anglo Nubian)
I've also never noticed more independance, bossiness or wariness around 3 years old, actually with our Togg bucks they have always gotten calmer as they get older and by 3 they are quite mature. :?
As Radena said, it could also be that they have a relatively plain colour variation - different shades of brown with the same white markings for every goat.

Cheers,
Cazz