Windows Update accting strange

I have a custom build desktop.
I have a maintenance and backup HDD drive where I boot from it and make my backups (system image and every Friday I do a data backup). This is a 1 T drive, used mainly for backup, but in an emergency I can work from it as it has all main programs on it.

My daily working drive is a SSD (C: for OS and programs) and a D: HDD for data.
After installing Win 7 64 Home Premium (on the SSD) with all latest drives and some programs, I ran the so called SP2 witch install all updates till last April. Then I run the manual Windows Update, it found some updates and installed them.
Then I cloned the two drives (SSD and HDD) to the backup HDD in two partitions.

Both are running well, except the backup drive. It doesn't run properly the Windows update.
On the backup drive, by the automatic update (only important and MS products, not Recommended updates), it finds the updates, and a icon appears on the notification area telling that there are updates to be installed. When I open Windows Update, there is nothing there.
If I choose to manually search for updates it runs for hours and hours and then I close it.

As once I had a similar problem and I deleted the C:\Windows\SoftwareDistribution folder and it began to work, I deleted it on the backup drive, but nothing changed.
Strange is that some important updates were installed automatically.
I've searched for help and I was taken to a MS site where I downloaded a WindowsUpdateDiagnostic.diagcab. When executed it opened the Diagnostic and troubleshooting wizard.
It found some problems but didn't fix all them.
Does someone knows how to fix the Windows Update on the backup drive?

Follow these instructions exactly.
First, set Windows Updates to never check for Updates.
Next reboot your computer, then install KB3020369, if not installed.
Then install KB3172605.

Windows updates should return to normal. You can then reset your updates to automatically check for updates if desired

https://support.microsoft.com/en-us/kb/3020369

https://support.microsoft.com/en-us/kb/3172605

Hi Mega,
on a further note
that code usually equates to access denied,
As a quick check set the back-up drive as primary.
if that fails follow these instructions
https://support.microsoft.com/en-gb/kb/968003

Roy

Thank you for your help.
- Pbcopter: The KB3020369 and KB3172605 were installed after setup. On my post I refer to it as SP2.
- Torchwood (Roy) I've followed the instructions and some issues were fixed. Ran antivirus and anti spyware and nothing found.

I'll return as soon as I get more informations.
Mega

Hi Mega,
thinking about it a bit more.
Might be that MS is classifying your backup as a seperate OS,
i can understand what your doing because i DONT follow a list of pre-determined questions/anwers.
However
you have 1 key and your using it REGULARLY on 2 different hardware ID settings, (which can be found in the MGAdiag report).
I suspect that MS might have "decided" you've reached the acceptable changes limit, and could be blocking them.


Roy

Roy, I don't think that having two Win 7 installed on different disks on same computer is the reason for the problem as I'm using this procedure for years without issues.
I've followed the instructions from https://support.microsoft.com/en-gb/kb/968003 without any results.
I've already wasted a lot of my time trying to fix this Win update issue, so I've decided to do a reinstall (update) on my installation.
I'll return for the feedback.
Thank you again.

What a headache.
I've done a reinstall (update) on my installation. As my Users folder is on drive D: I had to move (sysprep) it back to C: to be allowed to reinstall (update) on my installation. When done, moved (sysprep) Users folder back to drive D:. To do so I had to edit the register to clean the Update history.
After installing the SP2 (off line updates) I found out that my IE was 8 and I couldn't update it to IE 11 with the off line file.
And Windows Update wasn't working.

So I've made a image recover from the backup image that I have from the original basic installation.
Windows Update still didn't work.

After all it was my fault. As my computer isn't connected to any network, I had turned off some services that I thought that it wasn't needed, and one of them was BITS.

On Windows Update service, it says that it depends only on RPC (Remote Procedure Call)
On the WEB I've found that it also depends on:
- BITS (Background Intelligent Transfer Service)
- appidsvc (Application Identity)
- cryptsvc (Cryptographic Services)

Finally the WindowsUpdateDiagnostic finds no issues.
I'll let Windows update search for the updates.
I'll return with the feedback.

I give up!!!
Every time I run WindowsUpdateDiagnostic it says that it fixed some problem but if I run it again it will say it found a problem and has fixed. And Windows Update still doesn't work.
The final solution is to do a Clean Install (that I should have done in fist place).
How can it be so difficult to fix this this...