I my experience with 5.2, I found that if you are using an older version of Endpoint Encryption Manager to create 5.2 client installation set, you don't get the EE icon in the task bar even though the sbtraymanager exists. If you create the install set from 5.2 manager you will get the icon.
Hello. I'm an EEPC newbie myself but I too had an issue where the Tray Manger icon would not show up in the task bar. What I found is the registry key that launches the utility was missing. I manually created it and it's working fine now. Open the registry and browse to HKLM/Software/Microsoft/Windows/CurrentVersion/Run and check for the SafeBootTrayManager.exe key. If missing right click in the right hand pane and select "New, String Value". Call the string SafeBootTrayManager then modify the contents to read "C:\Program FIles\SafeBoot Tray Manager\SbTrayManager.exe"
Remember, there are two process that run in task manager:
SBTRAYMANAGER.EXE and SBCLIENTMANAGER.EXE. From your original post it looks like only the one is running.