Take 45 Seconds To Get To Desktop And 45 To Get Back In?

I currently run everything in admin mode. most of my games force me to. When my pc just turns on it is quick instant response time, but after running for half a day it becomes slowed.. When i click on a program to start you know how it goes to a lightey darkend screen and the yellow dialog box asking to run the program? Well this is how it works. i get a full black screen for about 15 seconds. then the yellow dialog box then the black screen again for 15 seconds. this is on any of my programs. then back to desktop then the program starts. and not even then does the program really start takes about 15 more seconds then black screen then the program starts running. BUT it still isnt.. the screen goes black, then goes to a lighter shade of black, then dark black, then lighter shade of black then the program starts time elaspes 45 seconds or so.. this is for any program.. and when this occurs the black screens i get this EEEEEEEEEERRRRRRRRRR sound from my speakers and if something else is running say teamspeak they all disappear for that time till the program starts.

Also another way to see this issue is when i alt tab out. Takes 2 seconds when the pc is just start or before hand. now it coudl take 45 seconds to get to desktop and 45 to get back in. while this could also cause programs to stop responding and screws with the icon placement on my desktop. Another way of it showing is when i press on the start button and it takes up to 15 seconds to appear. or when i try to pull back up a web browser same amount of timeThis all start occuring after i placed in a second graphics card. although i cant understand why that woudl be causing the issue.restarting the machine is the ONLY way to get this to stop happening and it is truely fustrating i run a very high end computer.