Apologies for the necro posting, but I thought this information might be useful for others that might run into the issue I had.
After rebuilding my server's OS and reinstalling Start11, I ran into exactly the same issues with not being able to restart or shutdown from Start11's menu options, even after I had applied my above mentioned fix - this turned out to be a complete coincidence and not at all related.
I tried several tests and discovered that the shutdown/restart did work on the default built-in Administrator account. The issue lay with user accounts with Admin access. I noticed the difference between admin and built-in admin was that UAC was fully disabled for built-in. This lead me to look into the group policy settings for UAC, and I discovered that I needed to set the following policy to disabled:
Computer Configuration > Windows Settings > Security Settings > Local Policies > Security Options > User Access Control: Run all administrators in Admin Approval Mode
Once disabled, I was able to shutdown/restart using Start11 on my own admin account. Note: even dropping UAC on a user account to never notify, does not affect this policy.