After a long time I went back to the IPython Shell.
I received some comments telling that it had some issues with IDA Pro 5.5 so I started to play with it.
The issue is not related to the IDA Pro version but with IDAPython version installed.
Starting from IDAPython 1.2 there's a "script timeout" value. This is why there's a little msg box telling you to wait because a script is running.
Since the IPython shell script doesn't end, as soon as you type something in the console, IDA blocks, and you can't move the window or anything.
This timeout value can be increased to avoid blocking IDA, but if you keep the shell opened for a long time, the timeout value may be reached.
Since IDAPython 1.4, you can disable this timeout value and work with the shell without problems. [1]
So I upgraded the script to automatically set up the timeout or disable it based on the IDAPython version you have installed.
You can still get the script here
If you find any other issue please let us know.
Enjoy!
[1] - http://code.google.com/p/idapython/issues/detail?id=50