Built new pc and applications load slow

I just built a new PC with i3 sandy bridge, gtx550 ti, 500 gb hdd, asrock H61M-VS mobo, 4 GB PNY 1333 mhz and basic dvd rom drive. Everything works fine except applications load extremely slow or when trying to install a program there is some sort of hang up in the pre installation process. Games seem to work fine once loaded. Any ideas?
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  1. I forgot to mention shutting down and restarting seems to take a long time too.
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