Both logs look very different as far as the Start Ups and I am not certain why, except you removed items from start up between the scans.
Did you do this? If so, then the second start up should have been faster because many items were removed.
Couple of things I note in both is your CA Security program does have a LOT of items associated with it...antivirus, antispy, firewall (hope you turned off the Windows Firewall, if not this will definitely slow a computer running two firewalls)
Now you have some things running which are not needed by most and which do use a lot of CPU....
Adobe Gamma Loader, Indexing Service, Viewpoint Manager Service. You can disable these from running at Start.
I recommend CodeStuffStarter to do this, do not use msconfig. Indexing and Viewpoint Manager Service run via Services and usually Adobe Gamma Loader runs from Start Programs.
How much RAM do you have installed?