This problem typically occurs when a new ISE version is installed. ISE uses the above registry key to determine whether or not ModelSim is installed, and it uses this information to enable or disable the simulation processes.
However, if the HKEY_CLASSES_ROOT\XLNXEDA\Products\DESIGNCNTR10\paths\VSystemPath key is not present in the registry, a default rule for finding ModelSim is used; this rule (on PC only) is specified to always assume that ModelSim is installed under the default path c:\Modeltech_xe\win32xoem.
To avoid this problem go to Edit -> Preferences, and select the "Partner Tools" tab to set the ModelSim path; the path entered here becomes the new value of the above registry key.
Under "Partner Tools", set the ModelSim Path to any value (where ModelSim is not installed), then close and re-open Project Navigator. The simulation processes will no longer be visible.