Windows 7: PC boots up fine, slows down, becomes normal after a few minutes

So here's my dilemma and I know I've never heard of this happening before. I have 2 internal drives in my tower, those being C: (main drive, obviously) and F:. F: was being a bit skittish so I decided to run chkdsk which fixed a few minor errors then moved on to booting into windows. Once it got into Windows, it loaded up the few startup items I have like Kaspersky Anti Virus, Steam, default manager and USB 3.0 monitor. No more than 4 items. Everything seemed fine and apparently booted up correctly. When I attempted to open a program, it didn't open for quite a bit of time and I couldn't open anything for a few minutes. Once the program finally opened, the PC started acting normally. I've run a full scan with KAV 2013 and did sfc /scannow to check integrity of the files and even did a chkdsk on C: which showed zero errors. No program I used to check the drive showed anything out of the ordinary.

This just seems like the oddest thing to me. I've heard of PC's slowing down after operating normal (in fact, I had this problem last week when I would close out of Steam which has recently been updated). My Microsoft Windows 7 Professional 64-bit SP1 is up to date and my Nvidia GeForce GT450 videocard is also up to date.

It's not the most horrible of situations, having to wait 5 or so minutes to start using my PC after Windows boots up but this is more a matter of curiosity. If someone has any ideas how to alleviate this problem, I'd be most gratified.

Here's my specs (via Speccy)

Operating System
Microsoft Windows 7 Professional 64-bit SP1
CPU
AMD Phenom II X6 1040T
Thuban 45nm Technology
RAM
8.00 GB Dual-Channel DDR3 @ 729MHz (9-9-9-24)
Motherboard
FOXCONN 2AB1 (CPU 1)
Graphics
VX2739 Series
Æ (1920x1080@60Hz)
1023MB GeForce GTS 450 (nVidia)
Hard Drives
1397GB Western Digital WDC WD15 EARS-60MVWB0 SATA Disk Device (SATA)
1863GB Western Digital WDC WD20 01FASS-00W2B0 SATA Disk Device (SATA)
Optical Drives
hp DVD A DH16ABLH SATA CdRom Device
Audio
Realtek High Definition Audio

Much thanks.

Hello Anthony and welcome to Seven Forums.

I think I'd do a clean startup (AKA clean boot) because it sure sounds like something might be causing a conflict at startup (like perhaps an anti-virus scan, defrag, etc.)

Troubleshoot Application Conflicts by Performing a Clean Startup

And you could open Task Manager > Resource Monitor to see if there's something hogging your CPU.

Resource Monitor

And one of the Forum experts has this troubleshooting guide with more suggestion.

Troubleshooting Steps for Windows 7

Establish a Clean boot before working through the other Troubleshooting steps linked above.

Ha! Been there, got the t-shirt on this one. It's very very likely a recent Kaspersky update. There's a crowd of us awaiting a fix for Kaspersky Internet Security 2013 with the 5 minute hang problem after a normal speed bootup. Temporary fix is to turn off System Watcher in the General Settings in KIS, I don't know where that is in KAV2013.

Replace KIS with Microsoft Security Essentials - Microsoft Windows