Yes, that was the problem, although when i tried your line it gave me an out of bounds error.
So instead i'm doing this: $FileNameCheck = ExpandEnvironmentVars($array[0])

I had read the help, and one of the Expressions had the %USERNAME% field in it, so i thought you could just use that without anything else.

Thanks.

So here's the updated code (smaller than the original too).
Code:
  Function TempArray($KBNumber)
	Break on
	$arrayfilehandle = FreeFileHandle()
	$filename = "$ScriptDir\UpdateFileList\" + $KBNumber + ".csv"
	If Open($arrayfilehandle,$filename) = 0 
		$line = ReadLine($arrayfilehandle)
		While @error = 0  
			$array = Split($line,",")
			$FileNameCheck = ExpandEnvironmentVars($array[0])
			$FileVerCheck  = $array[1]
			If GetFileVersion($FileNameCheck,"FileVersion") < $FileVerCheck 
				$NeedUpdate = 'Y'
				Exit
			EndIf
			$line = ReadLine($arrayfilehandle)
		Loop 
	$= Close($arrayfilehandle)
	EndIf
	$TempArray = $NeedUpdate
EndFunction