I'm seeing two issues.

1) Application shortcuts are missing/not being created in the left column of the Start menu. There are two pinned shortcuts and there is no problem with those.

Shortcuts were originally created in the left column. At some point, those present disappeared. The Configure / 'Show recently used applications' option is selected.

After I initially configured Start8, the only changes that I have made have been on the Style tab.

2) No Run history is being kept. If I use Run to run to run an app like Regedit, the next time that I use run, it is blank with no history.

I see that the Windows registry key for the history function is not in Win8 but adding it back makes no difference. If I use Run under Metro, it also is storing no history.