What supplements are you taking and how often? Is it possible you are missing something in your diet? Are you following recommendations from VeganHealth
2 things I would change if I were you:
1) Give up the shake before bed... they are full of sugar, are processed and definitely not a health food, despite their marketing. You will gain fat weight if you are eating too many calories. The beans, rice and nuts you are eating have enough protein (if the rice is whole grain, not white). Hopefully you are also including lots of greens in your diet for iron and calcium needs.
2) Run AFTER your workout.. not before. You need gylcogen stores to lift heavy and make muscle gains. Running will deplete those stores and make your lifting routine rather useless... you won't have the fuel or energy left to focus on the heavier weights that you should be.