You don't always see the other fish chase him or beat him up, it usually happens when you aren't watching.
What are the dimensions of your 45 gallon tank, post the Length x Width x Height please? I have a feeling it may be too short in length for 12 Malawi cichlids.
Brown algae on the rocks and the glass? It is probably diatoms and may/should go away after a few months.
Can you post a full tank view of your tank? We should be able to identify which Malawi cichlids you have and offer better suggestions for stocking your tank.