Whitelabel F-Droid & Privileged extension wont automatically update apps


I am very new here, so please excuse me if I am being obvious or rehashing something solved previously.

I am having a problem with the privileged extension giving auto-updates to my Fdroid Whitelabel version. It works with stock Fdroid, I have enabled push on my repo, I have added the various SHA-256 keys to the whitelist, either system or signed from Android studio and it comes up as enabled in the expert settings, so I think it is being seen by Fdroid client app but it just does not update.

I have even included a range of possible whitelabel options:

new Pair<>("com.mysite.appstore/org.fdroid.fdroid", "a40da80a59d170caa950cf15c18c454d47a39b26989d8b640ecd745ba71bf5dc"),

new Pair<>("org.fdroid.fdroid", "a40da80a59d170caa950cf15c18c454d47a39b26989d8b640ecd745ba71bf5dc"),

new Pair<>("com.mysite.appstore", "a40da80a59d170caa950cf15c18c454d47a39b26989d8b640ecd745ba71bf5dc"),

Above are examples I have repeated for testing with multiple keys.

I also see it boot on startup after the USB update.

We have full source for our version of Android (4.4.2) that we are using so I am preparing it as an incremental update and resigning the Fdroid app with ROM Keys(in Whitelist List of Privileged-Extension) and giving it privileged module status too but it still does not update.

Help would be very much appreciated.