As you have it now, it looks like the shutdown will be a continuous loop... everyone will be effected by it to... also please place your code in between the code tags (# on the post bar).

Might you give this a try
(untested)
Code:
$programpath="C:\Program Files\Pivotal\Relation\"
If Exist($programpath)
  $rc = MessageBox("Please wait while Relationship is uninstalled","ESI INT'L", 10, 0, 1)
  Shell 'C:\WINDOWS\uninst.exe -y -f "C:\Program Files\Pivotal\Relation" /passive'
  Sleep 6
  $rc = Shutdown("", "System is being rebooted to enable new settings.", 30, 0, 1)
Else
  ? $programpath + " Does not Exist"
EndIf