Try saving your theme, then do the following:
1 - Unload ObjectDock
2 - Go to "C:\Documents and Settings\USERNAME\Local Settings\Application Data\Stardock" folder, and delete the ObjectDock folder found there - this will clear the cache, and force ObjectDock to load with the program defaults.
Note - you may need to open My Computer, and go to "Tools > Folder Options > View tab" and select "Show hidden files and folders", then click "Apply" - which will allow you to access the Local Settings folder in the address above.
3 - Start Stardock Central > Tools menu > Settings > select the "MCP notification area support" option if not already selected > click OK.
4 - Reboot computer
5 - Start ObjectDock (the default docks will appear) > go to Dock Settings > load your saved theme > reboot machine to load all icons into the system tray dock
To the best of my knowledge, you should always see any icons that are visible in the Windows notification area, display in your system tray dock as well.
Note - if you do not have Stardock Central for some reason, you can do a search for "sdmcp.exe" file on your computer, and then create a shortcut to the file in your Startup menu - which will enable the notification area support.
I hope this clears it up.
If not, the icons that are not showing in the dock - yet are visible in the Windows notification area, may have either a setting or special function preventing their being displayed. 
