I've ran into a similar problem with Windows Update and the store not updating. However the issue I ran into is linked to SCCM task sequences not clearing some reg keys after completing. I've also seen a similar issue show up on non SCCM systems but I don't have enough data yet to know the root cause yet.
The issue was that the reg key for DoNotConnectToWindowsUpdateInternetLocations was left behind and possibly a few other in HKLM\SOFTWARE\Policies\Microsoft\Windows\WindowsUpdate
It also seems that Windows is caching the entries for those settings in a second spot now. HKLM\SOFTWARE\Microsoft\WindowsUpdate\UpdatePolicy\GPCache
I've found that stopping Windows update service and nuking out everything in HKLM\SOFTWARE\Policies\Microsoft\Windows\WindowsUpdate and HKLM\SOFTWARE\Microsoft\WindowsUpdate\UpdatePolicy\GPCache and then gpupdate then restart the windows update service clears up the issue.