Bloom's transformation into Dark Bloom was altered. In the original, purple orbs circle her and Darkar casts an flame of darkness which absorbs into her heart. In the special, Darkar shoots a beam of darkness at her.
In the original, one of Darkar's minions poses as Avalon to capture Bloom. In the special, Darkar himself poses as Avalon.
In the original, the Trix receive their Gloomix at Lightrock Monastery; in the special, they receive them in Darkar's castle.
Bloom is shackled in magic bonds and is standing instead of strapped down, before transforming into Dark Bloom.
Charmix does not exist in the special, due to the Winx's standard being renamed to Magic Winx Charmix. Ironically, Gloomix, the opposite of Charmix, still exists, but is not referred to by name.