The qtconsole prompt doesn't support most of what the regular IPython prompt does (which is an open issue). The configurable is also different.
The default value:
c.IPythonWidget.in_prompt = 'In [<span class="in-prompt-number">%i</span>]: '
You can change it with:
c.IPythonWidget.in_prompt = '<b><i>My Prompt </i>[%i]: </b>'
When the issue is addressed, it should behave exactly as you expect.