I ran into a little frustrating issue earlier with my Stand Alone installation on Windows 7 – my account had access to the Central Administration but some options weren’t there (like manage services on server) and others were giving me Access Denied. The ‘New Web Application’ was grayed out with a text saying I didn’t have access when I did a mouse over.
I was correctly set up as a farm administration and site collection administrator for the Central Admin. I tried rebooting and using other local accounts instead of the domain account – no luck.
So I started up the wizard with the intention of scrapping my newly built farm and simply re-create it but the wizard simply just ran over without asking me to remove it! The nice thing is that the automatic repair actually repaired my issue as well 🙂
October 29th Update: Actually, it looks like I was wrong. The issue came back the next day and the Wizard didn’t fix it – nor did I want to run the Wizard everyday ;). As it turns out, you need to ‘Run as Administrator’ Internet Explorer … what baffles me is that it sometimes work, sometimes not (and I had never ran IE as administrator… nor did I remove UAC on my Windows 7 build).