Computer Slows Down For 1-5 Mins About 5-20mins After Start Up

My computer, about 5-20 minutes after start up, slows down so much that I can hardly do anything for 5 minutes. I either A) wait it out till my computer goes back to running normally (takes 1-5 minutes) or hold my off button and restart (or actually shut down the normal way but it takes forever) but upon restarting the same thing happens again.I have no idea whats causing this. When its happening I check my CPU usage and its nothing unusual (0-30%). I have scanned with Malwarebytes (nothing), Microsoft Security Essentials (nothing), and Superantispyware (deleted a few adware cookies). Besides this slow down period, I see no other symptoms of malware. The only weird thing is for some reason I always get PC Issue in the bottom right hand corner that says Windows Defender/MSE is off, and asks me to turn one of them on, but I already have MSE running. I click the issue and tell it to turn on and update MSE, after which it stops bugging me but it comes back at least sometimes after I restart.The computer: a 2-3 year old dell laptop, been dropped a couple times but I've never had that cause problems before, windows 7.