For those of you being involved in a few Windows 8.1 deployment projects already (I have), you have probably stumbled into that setup behaves a bit differently in Windows 8.1 than it used to do in Windows 8. So far no fix has been announced, but I'm hoping there will be one-.
Shorthand, Microsoft kind of broke the Windows 8.1 GA image, and the result is that the Start screen items are missing for the built-in Administrator account, which of course is a royal pain when you want to prepare a reference image.
So far Microsoft seems not very interested in fixing this issue, despite several customers reporting the bug. Instead of providing a fix, they recommend Enterprise customers to ditch their current deployment methods and start using audit mode when preparing their reference image. This is of course beyond stupid. Most (if not all) enterprise organizations, are not using audit mode during their deployment. It's more or less only OEM's and system builders that uses that feature of the Windows Setup.
Workaround – Use the original Windows 8.1 RTM release.
The Start screen is only broken in the GA release of Windows 8.1, build 6.3.9600.16408 (?????SW_DVD5_SA_Win_Ent_8.1_64BIT_English_MLF_X18-96759.iso). The first RTM release of Windows 8.1, build 6.3.9600.16384, that was released before October 18, don't have the issue. So if you are lucky enough to have a copy of that one around, you're good to go.
Disclaimer: I don't know if using the original Windows 8.1 RTM release is supported by Microsoft. I only know it works, and doesn't have the Start screen issue.
Also, for a really interesting read, and for some additional background info to this post, I recommend reading the following forum threads:
Below you see the difference between the GA version of Windows 8.1 vs. the RTM version of Windows 8.1: