Thanks HardKnoX, figured it was something easy like that. I've edited my posts with code tags, and per Steven's excellent recommendation, here is one more script that you can add to the end of the removal scripts I posted which will check and correct the chkdsk run on every boot. Can be run separately as well of course.
<?xml version="1.0" encoding="utf-8"?>
<ScriptExport xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns="http://www.kaseya.com/vsa/2008/12/Scripting">
<Procedure name="KB2823324 Autochk Detection and Fix" treePres="3" id="482576512" folderId="32119231541794396193144183">
<Body description="">
<If description="">
<Condition name="CheckRegistryValue">
<Parameter xsi:type="StringParameter" name="RegistryPath" value="HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\BootExecute" />
<Parameter xsi:type="EnumParameter" name="Condition" value="Equals" />
<Parameter xsi:type="StringParameter" name="Value" value="autocheck autochk *" />
</Condition>
<Then>
<Statement description="Set the specified registry value - Regedit displays keys as folders and values as documents." name="SetRegistryValue" continueOnFail="false">
<Parameter xsi:type="StringParameter" name="RegistryPath" value="HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager\BootExecute" />
<Parameter xsi:type="StringParameter" name="Value" value="autocheck autochk /k:C *" />
<Parameter xsi:type="EnumParameter" name="DataType" value="MultiString" />
</Statement>
</Then>
</If>
</Body>
</Procedure>
</ScriptExport>