This problem perplexed us recently, when launching a published desktop from a thin client (Igel in our case) microsoft office and other applications when in full screen would hide the taskbar.
This behavior was not seen on fat clients using the 10 and 11 windows ica client.
The Fix was found in the following reg key,
HKEY_LOCAL_MACHINESOFTWARECitrixCtxHookAppInit_DllsMultiple Monitor Hook
configuring this reg dword value to 0 and restarting the citrix servers fixed the problem.