I still have the exact same problem on Ubuntu 11.10 Oneiric.
And launching "unity --reset" doesn't help.
The problem is annoying and reproductible.
I open (let's say) a terminal, a firefox, an instance of Eclipse. 
When they're all maximized, everything works fine.
If i minimize a window, then i alt-tab immediately (or later) to this application, the maximized position is not well restored : it's just like the window is restored to the the 0x0 coordinate instead of just below the "unity main control bar".

% unity --reset

































Checking if settings need to be migrated ...no
Checking if internal files need to be migrated ...no
Backend     : gconf
Integration : true
Profile     : default
Adding plugins
Skipping upgrade com.canonical.unity.unity.01.upgrade
Skipping upgrade com.canonical.unity.unity.02.upgrade
Initializing core options...done
Initializing bailer options...done
Initializing detection options...done
Initializing composite options...done
Initializing opengl options...done
Initializing decor options...done
Initializing gnomecompat options...done
Initializing resize options...done
Initializing snap options...done
Initializing mousepoll options...done
Initializing place options...done
Initializing commands options...done
Initializing grid options...done
Initializing wall options...done
Initializing move options...done
Initializing vpswitch options...done
Initializing session options...done
Initializing animation options...done
Initializing workarounds options...done
compiz (expo) - Warn: failed to bind image to texture
Initializing expo options...done
Initializing ezoom options...done
Initializing staticswitcher options...done
Initializing fade options...done
Initializing scale options...done

Screen geometry changed:
   0x0x1920x1080

unity-panel-service: aucun processus trouvé
Initializing unityshell options...done
DEBUG 2012-01-09 12:55:10 glib <unknown>:0 Setting to primary screen rect: x=0 y=0 w=1920 h=1080
Setting Update "preview_scale"
Setting Update "speed"
Setting Update "timestep"
Setting Update "popup_delay"
Setting Update "icon_only"
Setting Update "highlight_mode"
Setting Update "highlight_rect_hidden"
Setting Update "alt_tab_forward"
Setting Update "alt_tab_prev"
Setting Update "alt_tab_right"
Setting Update "alt_tab_left"
Setting Update "alt_tab_detail_start"
Setting Update "alt_tab_detail_stop"
Setting Update "show_minimized_windows"
WARN  2012-01-09 12:56:09 unity.glib.dbusproxy GLibDBusProxy.cpp:255 Cannot call method InfoRequest proxy /com/canonical/unity/lens/applications does not exist
WARN  2012-01-09 12:56:09 unity.glib.dbusproxy GLibDBusProxy.cpp:255 Cannot call method SetActive proxy /com/canonical/unity/lens/applications does not exist
WARN  2012-01-09 12:56:09 unity.glib.dbusproxy GLibDBusProxy.cpp:255 Cannot call method InfoRequest proxy /com/canonical/unity/lens/commands does not exist
WARN  2012-01-09 12:56:09 unity.glib.dbusproxy GLibDBusProxy.cpp:255 Cannot call method SetActive proxy /com/canonical/unity/lens/commands does not exist
WARN  2012-01-09 12:56:09 unity.glib.dbusproxy GLibDBusProxy.cpp:255 Cannot call method InfoRequest proxy /com/canonical/unity/lens/files does not exist
WARN  2012-01-09 12:56:09 unity.glib.dbusproxy GLibDBusProxy.cpp:255 Cannot call method SetActive proxy /com/canonical/unity/lens/files does not exist
WARN  2012-01-09 12:56:09 unity.glib.dbusproxy GLibDBusProxy.cpp:255 Cannot call method InfoRequest proxy /com/canonical/unity/lens/music does not exist
WARN  2012-01-09 12:56:09 unity.glib.dbusproxy GLibDBusProxy.cpp:255 Cannot call method SetActive proxy /com/canonical/unity/lens/music does not exist
WARN  2012-01-09 12:56:11 unity.iconloader IconLoader.cpp:509 Unable to load contents of file:///usr/share/icons/unity-icon-theme/places/svg/category-installed.svg: Erreur à l'ouverture du fichier : Aucun fichier ou dossier de ce type
WARN  2012-01-09 12:56:11 unity.iconloader IconLoader.cpp:509 Unable to load contents of file:///usr/share/icons/unity-icon-theme/places/svg/category-available.svg: Erreur à l'ouverture du fichier : Aucun fichier ou dossier de ce type