I have both the 1/4" Janome that came with the machine (I have a humble 3160QDC) whihc I didn't like becuase it was flayed a bit at the toe and would not do a proper 1/4". I bought the multi-part foot what has the 1/4" flange, plus the stitch-in-ditch flange.
the 1/4: flange works great, sits right up against the plastic foot. I do a measuring test for each new fabric/thread and adjust the needle position if necessary.
Maybe the foot that came with your machine had a bent flange.
Good luck