For example, invoking tab completion causes the prompt number to advance by several numbers ( see here). Of course, I've found other issues working with IPython in Emacs on Linux as well.
Interestingly, all the In's print out after I kill the IPython process, which is obviously not useful. However, input prompts still do not show up right, as you say. I can get things somewhat better by making sure that the command used to run IPython from within Emacs is python.exe -i /path/to/Python/Scripts/ipython_script.py. Simply running ipython.exe as an inferior Python buffer doesn't work properly - you can type things in the buffer but there are no In prompts or output. Since this site is primarily here to provide help in the use of IPython, and host discussions about current and future features, make sure that it is clear how comments are relevant to the original post or the previous comment. The visitors to /r/IPython come from very different backgrounds and some even have little programming experience. IPython Notebook Viewer Post your notebooks here, (from gist on github for example).Help chat room (The new official help line).With new additions like the IPython Notebook, which runs in a browser, and the Notebook Viewer, IPython is a scientist's best friend. Since then it has grown in popularity, and gaining to the ability to make XKCD styled plots using matplotlib hasn't hurt. IPython (now Jupyter) was originally started by Fernando Perez as a way to improve the Python work flow for scientific computing.