(1) Because her proposal had been rejected , she was depressed.
Two actions have occured. They are both completed actions in the past. First, her proposal was rejected. Next, (after she learns of the rejection) she is depressed. One action happened as a result of the other.
(2) Because her proposal has been rejected , she is depressed.
Here we have state of being (she is depressed) that is occurring in the present, and an action that has taken place. The sentence could also be written: Because her proposal was rejected, she is depressed, but has been rejected gives the sense that the proposal was rejected very recently.
I hope this is helpful,
Student or Learner