Hi Creed,
I haven’t seen this issue pop up. Just to be sure you’re updating from 5.0 to 5.1? Please post a picture of what the black square looks like. (Maybe its thickness/aliasing might give some clues?) Also, are you able to reproduce this in a new project?
+Since you say it’s ‘most’ of the opacity textures, is there anything similar about the misbehaving group?
Just some ideas!