Is there any chance you have the option in the View menu for "Put icon in tool tray" turned on? If you do, then PingPlotter is *supposed* to dissapear from the task bar, and an icon should show up in the tool tray area.
If you were previously using 2.41 or earlier, note that the icon changed in the 2.50 release, so make sure you're looking for the right icon. It should look something like this (although smaller and a bit different):
If this isn't the case, please let us know so we can dig further.