I tried running simple example files from the beamer package with always the same results. Here is what I get when I try to pdfLaTeX as usual a file that I used to run successfully in old MiKTeX versions or any other beamer file:
This is pdfTeX, Version 3.1415926-2.4-1.40.13 (MiKTeX 2.9 64-bit)
entering extended mode
(...)
======================================================================
starting package maintenance...
installation directory: "C:\Program Files\MiKTeX"
package repository: http://bay.uchicago.edu/tex-archive/sys ... /packages/
lightweight database digest: 4ab85e12cf451ec0bb6c3eaae69a6936
going to download 2560891 bytes
going to install 336 file(s) (1 package(s))
downloading http://bay.uchicago.edu/tex-archive/sys ... r.tar.lzma...
2566412 bytes, 399.40 KB/Sec
visiting repository http://bay.uchicago.edu/tex-archive/sys ... /packages/...
repository type: remote package repository
loading lightweight database...
downloading http://bay.uchicago.edu/tex-archive/sys ... 9.tar.lzma...
137358 bytes, 506.18 KB/Sec
pdflatex.exe: Windows API error 5: Access is denied.
pdflatex.exe: Data: C:\
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! LaTeX Error: File `beamer.cls' not found.
Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: cls)
