Odd listing with .vmx file

I'm hardening some VMs, and I have a script that I found online (can't remember who it was from, but probably LucD).  The script is not the issue, but the csv file that the script references has some of these lines:

floppy0.present,FALSE

ide0:0.present,FALSE

logging,TRUE

Well, the script seems to work fine, but then when I check the .vmx file with (Get-VM "Name").extensiondata.config.extraconfig, the $_.key for any line that has to do with virtual hardware does not appear.  I don't think this is really a scripting issue, but this section is so active, that maybe someone can lead me in the right direction, and I'm using PowerCLI to edit the settings, so I guess it's relevant.  There are multiple lines, and everything appears fine except for hardware related lines:

floppy0.present,FALSE

floppy1.present,FALSE

ide0:0.present,FALSE

ide0:1.present,FALSE

ide1:0.present,FALSE

ide1:1.present,FALSE

parallel0.present,FALSE

serial0.present,FALSE

Other lines appear when I retrieve them:

isolation.monitor.control.disable,TRUE

isolation.tools.ghi.autologon.disable,TRUE

isolation.bios.bbs.disable,TRUE

isolation.tools.getCreds.disable,TRUE

Even if I "edit settings" > Options > Advanced | General > Configuration Parameters, and add a line there, I can't retrieve it with powershell (only hardware lines)  if I directly edit the .vmx file and copy it back, those lines don't show up with powershell, but they will show up if I look at the .vmx file on Windows with Write, or some other text editor. 

Has anyone experienced this?  More importantly, does anyone know what I'm doing wrong?

The script is here, and there is a CSV file that I use, with the examples that I listed, it has the Key,Value columns correctly

#This line imports the key and value pair for the .vmx setting

$import = Import-Csv "C:\STIGapply\STIG_current.csv"

$VMs = Get-folder STIG | Get-VM "*clone"

$vmConfigSpec = New-Object VMware.Vim.VirtualMachineConfigSpec

Foreach ($item in $import) {

$extra = New-Object VMware.Vim.OptionValue

$extra.Key = $item.Key

$extra.Value = $item.Value

$vmConfigSpec.extraconfig += $extra

}

Foreach ($vm in $vms) {

$vm.ExtensionData.ReconfigVM($vmConfigSpec)

}