I too am having the problem. I think its from using the trainer options. Possibly using the jump height modifier (Super Jump). Certain actions and cut-scenes can be bypassed by using the Super-Jump and/maybe/or Teleport options. I am going to re-play the game, unless anyone has a game save they would like to upload (preferrably around the Stygian worm dude), from Version 1.1 - as all the savegames I have tried from a save-game site were all "corrupted", probably due to version mismatch.
I dont want to start Darksiders II before I finish the first Darksiders. Unfortunately I can't try the suggestion of morphing into that big red dude to try and get my tertiary weapons usage back because in a fit of anger I deleted all my savegames. Back to the start of the game for me