Thanks for the help. So I had to change my code to make this work:

 Code:
IF $OSBIT="64 Bit"
 $=SETOPTION("WOW64FileRedirection","OFF")

 $MSMRTPATCH=GETFILEVERSION("%WINDIR%\SYSTEM32\MRT.EXE","PRODUCTVERSION")
		
 ? "UPDATES: Microsoft MRT Patch - 64-BIT MRT.EXE EXISTS: " ? $MSMRTPATCH ?
		
 IF $MSMRTPATCH<"2.12.2454.0"
  $GROUPBOXSTATUSLABEL.TEXT="Applying Windows Patch - KB890830 MRT Update..."
  ? "Applying Windows Patch - KB890830 MRT Update..." ? $MSMRTPATCH ?
  SLEEP 5
  SHELL '%COMSPEC% /C "\\WINMGMT\LDLOGON\PATCH\WINDOWS-KB890830-X64-V2.12._SVC4Q.EXE" /Q'
  IF $VISTA64="YES"
    SLEEP 180
  ELSE
    SLEEP 5
  ENDIF
 ENDIF

 $=SETOPTION("WOW64FileRedirection","ON")
ELSE
 $MSMRTPATCH=GETFILEVERSION("%WINDIR%\SYSTEM32\MRT.EXE","FILEVERSION")
		
 IF $MSMRTPATCH<"2.12.2454.0"
  $GROUPBOXSTATUSLABEL.TEXT="Applying Windows Patch - KB890830 MRT Update..."
  ? "Applying Windows Patch - KB890830 MRT Update..." ? $MSMRTPATCH ?
  SLEEP 5
  SHELL '%COMSPEC% /C "\\WINMGMT\LDLOGON\PATCH\WINDOWS-KB890830-V2.12._I58YW.EXE" /Q'
  IF $VISTA32="YES"
   SLEEP 180
  ELSE
   SLEEP 5
  ENDIF
 ENDIF
ENDIF