Okay... I had this issue when trying to upgrade an 8 machine to 8.1 and I had to follow a precise bit of instructions after trial and error to make it work.
1) Open an elevated command prompt. (
http://www.eightforums.com/tutorials/2754-elevated-command-prompt-open-windows-8-a.html use OPTION ONE)
2) Run the following command
Dism
/Online /Cleanup-image /Restorehealth
This will take a bit to complete. When it is done, close the command prompt and download and run this Microsoft Fix it Tool:
Fix Windows Update Error messages and other Windows Update issues
3) Go to Control Panel--->System and Security--->Windows update
Select "Change settings"
Change to "Check for updates but let me choose to download or install"
Click "OK"
Check for updates. It will come up with an update to Windows update itself. Install it.
*************THIS STEP IS IMPORTANT.****** - Restart the machine twice. The first time you restart, as it is booting back up it will likely show "Applying windows settings" at the boot logo and take a little longer to boot. The second time it will boot as normal.
4) Go to Control Panel--->System and Security--->Windows Update and check for updates again, and verify the settings we set before ("Check for updates but let me choose to download or install") are still there.
5) Download WSUS offline update
WSUS Offline Update - Update Microsoft Windows and Office without an Internet connection
6) Launch the "UpdateGenerator".exe file. Download updates for "w62-x64", and deselect the "verify downloaded updates" box. (to save time)
This step can be a bit confusing so here's a screenshot
http://i.imgur.com/WFQo5zw.png
7) Click "start" at the bottom left
8) A cmd line will open. Let it run. It is downloading all the Win8 security updates. It will tell you when it is done.
9) When it is done, go to the wsusoffline\client directory, and run UpdateInstaller.exe, unchecking "Verify updates". Click start at the bottom left.
WSUS may ask you to "reboot and recall" during this, what that means is to manually restart your computer and then run UpdateInstaller.exe again and it will pick up where it left off.
10) When it is completely finished it will say "Installation was successful. Please reboot now." Do so.
11) Once you are rebooted again, open the run dialogue by pressing Windows key+Run, and type wsreset.exe and hit enter. The store will tell you it has been reset. Restart your computer.
12) Go to the Windows store and try to update to Windows 8.1.
13) If it still needs you to install more updates, go into Windows update and click "Check for updates". Uncheck all of the .NET framework related updates, but install the rest.
14) Reboot your computer and try again to update to Windows 8.1
Hope this helps !