[Plugin: WordPress Automatic upgrade] Problem display, categories link

I tried to upgrade 2.61-2.7 everything seemed ok,when I went to admin left column links were not there just says Dashboard the bottom was empty.
One thing I have noticed with the plugin it tells you to click on a link which open another window,this is confusing,it should be smooth process step1,2,…not open another window close, come back,..

I had to manually clean all my directories and install 2.7.now my categories did not work I had my url as /category/post name it gave me 404 error.

i had to change to post name to work.