I have had the same problem; in addition, some of my favorites - Menu Meters and Application Switcher Menu behave the same way - so both Apple menu bar and 3rd party icons are not behaving. The problem did not occur until I installed the OS 10.8.2 update. When the problem ocurred, I:
1. Ensured that my system preferences in "Secutity and Privacy" were set to allow any applications.
2. Ensured that the "display icons" in each item I wanted were set to do so; this often resulted in a prolonged spinning beach ball before the setting would finish.
3. Eliminated all old system preference panes I had been using - Growl, Microsoft Keyboard (part of anold Intellipoint installation) and others, and ensured I had the latest versions of Menu Meters and ASM.
4. Installed the latest Microsoft Mouse preference pane because I use a Microsoft Trackball Explorer.
5. Removed and reinstalled all current 3rd party preferece panes (something that had worked for much earlier OS 10 updates).
6. Ran "Preferential Treatment" and removed two corrupted preferences (they were not preference panes).
7. Removed old startup items.
8. Downloaded the OS 10.8.2 combo update, and reinstalled it.
9. Repaired permissions in Disc Utility.
Now, the menu bar items load properly on about 1 of 3 startups. The startup sequence seems to fiffer. Sometimes, I get the arrowhead for the cursor immediately once I have entered my security code, and the desktop will appear all at once, with my walpaper, the finder open, and all menu bar icons displayed.
Sometimes I get a spinning beach ball instead of a cursor arow, and the desktop and finder load very slowly - usually without the icons. Often, the Spotlight icon will appear and disappear.
Sometimes I get the cursor, then the wallpaper and menu bar, then the hard drives I always dislay - there is a delay while the HD data comes up; then the dock - and sometimes I then get the menu bar icons, but usually not.
These different behaviors occur without my making changes from startup to startup.
I hope someone can help.