So I went ahead and killed the skype-launcher process and launched skype-wrapper in the terminal.

I have the same behavior (the messages I receive at Skype won't show up at the Ubuntu Messaging Menu and I get regular skype notifications instead of the unity notification popup which only woirks for skype friends getting on or offline).

here is the output I got when I ran skype-wrapper from terminal:

thiagob@hmpc:~$ skype-wrapper
/usr/lib/python2.7/dist-packages/gobject/constants.py:24: Warning: g_boxed_type_register_static: assertion `g_type_from_name (name) == 0' failed
  import gobject._gobject
Starting skype-wrapper
/usr/lib/python2.7/dist-packages/gobject/constants.py:24: Warning: g_boxed_type_register_static: assertion `g_type_from_name (name) == 0' failed
  import gobject._gobject
INFO: Initializing Skype API
INFO: Starting Skype process
INFO: Waiting for Skype Process
INFO: Attaching skype-wrapper to Skype process
The program 'indicator-applet-skype.py' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadWindow (invalid Window parameter)'.
  (Details: serial 14 error_code 3 request_code 25 minor_code 0)
  (Note to programmers: normally, X errors are reported asynchronously;
   that is, you will receive the error a while after causing it.
   To debug your program, run it with the --sync command line
   option to change this behavior. You can then get a meaningful
   backtrace from your debugger if you break on the gdk_x_error() function.)
Applet closed
API crash detected
Restarting skype-wrapper
/usr/lib/python2.7/dist-packages/gobject/constants.py:24: Warning: g_boxed_type_register_static: assertion `g_type_from_name (name) == 0' failed
  import gobject._gobject
INFO: Initializing Skype API
INFO: Waiting for Skype Process
INFO: Attaching skype-wrapper to Skype process
The program 'indicator-applet-skype.py' received an X Window System error.
This probably reflects a bug in the program.
The error was 'BadWindow (invalid Window parameter)'.
  (Details: serial 14 error_code 3 request_code 25 minor_code 0)
  (Note to programmers: normally, X errors are reported asynchronously;
   that is, you will receive the error a while after causing it.
   To debug your program, run it with the --sync command line
   option to change this behavior. You can then get a meaningful
   backtrace from your debugger if you break on the gdk_x_error() function.)
Applet closed
API crash detected
Restarting skype-wrapper
/usr/lib/python2.7/dist-packages/gobject/constants.py:24: Warning: g_boxed_type_register_static: assertion `g_type_from_name (name) == 0' failed
  import gobject._gobject
INFO: Initializing Skype API
INFO: Waiting for Skype Process
INFO: Attaching skype-wrapper to Skype process
Exception in thread Skype4Py API thread (most likely raised during interpreter shutdown):
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 551, in __bootstrap_inner
  File "/usr/lib/pymodules/python2.7/Skype4Py/api/posix_x11.py", line 315, in run
  File "/usr/lib/python2.7/threading.py", line 403, in wait
  File "/usr/lib/python2.7/threading.py", line 258, in wait
<type 'exceptions.TypeError'>: 'NoneType' object is not callable
/usr/lib/python2.7/dist-packages/gobject/constants.py:24: Warning: g_boxed_type_register_static: assertion `g_type_from_name (name) == 0' failed
  import gobject._gobject
INFO: Initializing Skype API
INFO: Waiting for Skype Process
INFO: Attaching skype-wrapper to Skype process
/usr/lib/python2.7/dist-packages/gobject/constants.py:24: Warning: g_boxed_type_register_static: assertion `g_type_from_name (name) == 0' failed
  import gobject._gobject
INFO: Initializing Skype API
INFO: Waiting for Skype Process
INFO: Attaching skype-wrapper to Skype process
INFO: Attached complete
INFO: Initializing online status for users
INFO: We are offline
INFO: We are offline
INFO: We are offline
INFO: We are offline
INFO: Checking unread messages
INFO: Checking online status changing users
INFO: Checking online presence
INFO: Checking file transfers
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence
INFO: Check if Skype instance is running
INFO: Checking online presence