I've just read your graphs again. It looks like when you extend the stiffening plate all the way to the end of the flat plate, at the corner joint, it causes the stresses to shift from the horizontal flat plate and concentrate in the vertical flat plate.
In other words, while the stiffener is short, both the horizontal and vertical flat plate are able to split the Secondary bending stresses at the corner joint 50% each.
When the stiffener extends all the way to the end, the top flat plate becomes more constrained, therefore its bending stress is shifted to the vertical flat plate, meaning that the vertical flat plate takes 100% of the corner joint bending stress, hence a higher stress.
For this specific geometry, shortening the stiffener or using a different profile (i.e. Triangle, 45° chamfer) will allow the stresses at the corner junction to distribute more evenly across both sides of the corner joint. But watch out for the can-opener issue described by 3DDave.
If after trying these ideas, this still results in excessive bending stress on both sides of the corner joint, a reinforcement element that wraps around the corner joint may be needed (or increase in flat plate thickness). Appendix 13 is good for making this assessment.