So, after testing on both stable and frontline, using levels 1-5, I can confirm Second wind does indeed interrupt your natural EP regen for 1 second if you activate it (landing a basic attack). But, it's definitely not bad, if at level five hitting multiple enemies at once. It holds back EP regen builds early stage though, I think.
So in the case that this is still considered a bug,
The weapon I was using to do basic attacks was the Flower whip, and only each of the earth spells to deplete EP to test, and on each of the monsters in the "Mushroom Caves".