Flushing application output automatically starts a new line

When I call fflush(stdout) or std::cout << std::flush, the output in the application output pane automatically starts a new line.
I am printing out the progress of my program on the same line with '\r', if I don't flush the output, the progress is not printed until it finishes. If I flush output, then application output pane just starts a new line making program print many lines of progress output.

If I run my program in terminal, it does not have this problem, all the outputs are printed out on the same line.