I let them stack, just because there is also the possibility to have a shocking flaming sword that does an extra 2d6 damage (electricity and fire), so from a balance point of view there's nothing against it.
Someone somewhere (in another thread some time ago) pointed out that it wouldn't make sense to have "hotter" flames but I think it's the same like a fireball cast by a 5-th and a 10-th level mage.
Greetings
Firzair