I've noticed that the iPython console seems to break/change at least some of IDA's console functionality. Specifically, I've noticed that the default IDA console/output window no longer prints the result of a statement being evaluated.
eg, this is what IDA does normally:
Python>idaapi.get_screen_ea()
0x1801c5977
But with iPython running/installed, the address does not get printed out. It seems that iPython is swallowing these prints or something. Also, related (or maybe a side effect?) is that the IDA console will no longer print integers as hex by default. I think this was maybe some hook they had on STDOUT but I am not sure.