It's possible the taskbar is being hidden. You might check how the taskbar registry keys (esp. the AutoHide entry) are set:
[HKEY_LOCAL_MACHINE\Software\Microsoft\Shell\OnTop]
"Default"=dword:1 ; [1=keep taskbar on top]
;
[HKEY_LOCAL_MACHINE\Software\Microsoft\Shell\AutoHide]
"Default"=dword:0 ; 1=minimize taskbar to a line when not in use
If the problem persists, please let us know what build of CE you're using (ADS release number 700111-1xxxx or build#/size). You might also email the ADSLOAD.REG to us for evaluation.