Disabling Minimal Download Strategy from PowerShell but still shows feature as "Activated".

Question

I have an interesting issue with the Minimal Download Strategy feature in SharePoint 2013. I have a script in place which will disable this feature on all sites in all site collections on our Farm. The script has been working fine and we schedule it to run
daily at 8PM so that any new sites that get created will have this feature shut off, in case the person who created it forgot to disable it.
As of recently, I've noticed while the script appears to be working fine, we are seeing that new sites are still showing the feature as activated in the "Manage Site Features" page. If I re-run the script, it shows that the feature is disabled
and won't do anything. The script basically steps through all sites of all site collections in our default web application and if the MDS feature is enabled it disables it. Simple enough.
So why am I now seeing sites that show the feature is Activated even though it is disabled? I've checked this by noting the URL that the site uses and it does not load pages from the "_layouts/15/" location. 
The reason we have to turn this feature off on all sites is because we allow external users to access our SharePoint through a secure proxy. With this feature enabled, we have constant problems with pages not loading properly or generating javascript errors.
Anyone have any insight into this?

Answer 1

Here is the script we are using. As I mentioned, it works fine. It disables the the "Minimal Download Strategy", however when you go to the site settings it shows the feature is activated. 
# This PowerShell script will check all sites of each site collection in
# the default Web Application to see if the MDS (Minimal Download Strategy) 
# feature is enabled and if so it will turn it off.
# This script should be scheduled to run once a day to ensure this feature
# is always disabled.
# Register SharePoint Snap-In
$ver = $host | select version
if ($ver.Version.Major -gt 1)  {$Host.Runspace.ThreadOptions = "ReuseThread"}
Add-PsSnapin Microsoft.SharePoint.PowerShell
Set-location $home
Write-Host "Script Running at "(Get-Date);
$Default_WebApp = "http://vmsp2k13app.phs.org"
# Get all Site Collections in the default Web Application
$SPSites = Get-SPSite -WebApplication $Default_WebApp
#Cycle through each Site Collection and its Webs (sub-sites)
ForEach($Site in $SPSites){
Write-Host "";
Write-Host "Checking Site-Collection: " $Site.Url;
ForEach($Web in $Site.AllWebs)
Write-Host "";
Write-HOst "    Checking Sub-Site: " $Web;
If($Web.EnableMinimalDownload -eq 1)
Write-Host "        Minimal Download Strategy is Enabled for this site!";
Write-Host "        Disabling....";
$Web.EnableMinimalDownload = 0;
$Web.Update();
Else
Write-Host "";
$Web.Dispose();
$Site.Dispose();