I've been trying to use the IPython notebook support today, and have noticed a few issues:
SHIFT-ENTER will now advance to the next code block, but doesn't always execute the code. Possibly related - the In  will change to In [*] when it's executing, but often changes back to In , instead of In  (or whatever step in the execution chain it happens to be). I can see that it WAS executed, because if it happens on an import based code block I can still use the libraries that should have been imported.
Selecting a code block on the screen will often cause the display to jump around - I do not want the next code block to jump to the top of the window just because I clicked on it, or advanced to it.
Opening a .pynb file does not offer to 'open in a new window'. So I happen to have a project that was created with OXdbe that I am now editing in PyCharm, which consists of SQL Scripts - nothing python related. If I have that open and try to open a .pynb file it opens fine, but will open in the same window as the SQL scripts project. Any code completion is then broken for python libraries where the property or method hasn't yet been used in the script. There is no way for me to otherwise open a new PyCharm window for those .pynb file on Windows (that I know of).
The color scheme for errors (red/green/blue) isn't very readable with the darker theme - it also doesn't appear to use the same font as the rest of the editor window.