Elemental damage bonus from Enchantress’ Amplification skill is not applied when the character has another elemental bonus active (that is displayed in the details window). Tested with Spectral Blade - Flame Blades, Black Hole - Absolute Zero, and Wave of Force - Arcane Attunement.
On the attached video Enchantress is close to the character, has Amplification selected (+9.33 bonus to all elements), and this bonus falls off when the character starts attacking with Flame Blades. The same effect can be observed for Absolute Zero. Note that the video also showcases another, unrelated issue with Stone of Jordan, described in another bug report.
Arcane Attunement on the other hand, while seems to have a quite similar mechanic, doesn’t affect the numbers in the details window, and doesn’t break Amplification.
Video: SoJ + Flame Blades - YouTube