Idle Process Freezing

The Problem:
When my computer goes into idle process/sleep, it freezes completely. It also freezes whenever I run a full system scan with MSE, regardless of what I'm doing to prevent idle process(moving the mouse, pressing keys etc). This problem also occurs when I run scans in Safe Mode.

My Computer:
OS: Windows 7, 64 bit
Processor: AMD FX(tm)-4100 Quad-Core, 3.6 GHz
RAM: 8 GB
Graphics: NVIDIA GeForce GT 610
-->Currently running two monitors
Hard Drive: Hitachi SATA 1TB
AntiVirus: Microsoft Security Essentials, most current version
AntiSpyware/Malware: SUPERAntiSpyware Free Version, no real-time protection
Other Precautions: Regularly run the commands: sfc /scannow && cipher /w:C: && CHKDSK (in safe mode)

Things I've Tested:
MSE Full Scan, SAS Full Scan, and Command Promp scans in Safe Mode: Freeze
MSE Full Scan, SAS Full Scan, and Command Promp scans in Normal Mode: Freeze
SAS Full Scan in Safe Mode: No freeze, low threat Adware detected
Command Prompt scans in Safe Mode: No freeze, no problems detected
MSE Full Scan in Safe Mode: Freeze
MSE Full Scan in Normal Mode: Freeze
Allowing Computer to go to sleep, no scans: Freeze
Using program GhostMouse to keep mouse constantly moving(no idle process): No freeze
Installing Norton 360 and running Full Scan in Safe Mode: No freeze, nothing other than low threat Adware detected (I uninstalled it afterwards, dont like it)

Every time MSE froze the computer, it stopped on a different file, however I forgot to record the specific files. I recall one of them being related to a Steam App.

In Conclusion:
This problem isn't critical, however it can be extremely annoying to deal with. My first conclusion was a virus freezing the computer when detected, however the safe mode testing seems to disprove that. Next someone suggested it might be a conflict between SAS and MSE, though once again, safe mode testing seems to point to a problem with MSE itself. Any ideas you guys could give me would be greatly appreciated.

Hello MKalashnikov and welcome to Seven Forums.

Have you tried uninstalling MSE and reinstalling a fresh copy? Perhaps the original install was damaged or corrupt in some way and didn't successfully complete. If that doesn't help you might want to see if an installed application or process is causing the freezes. You can do this by performing a Clean Startup (aka: Clean Boot.)

Troubleshoot Application Conflicts by Performing a Clean Startup

Another possibility is damaged or corrupt system files. You could try running a System File Checker scan from an elevated command prompt (Option Two.)

SFC /SCANNOW Command - System File Checker

And if still no joy, one of the Forum experts prepared this troubleshooting guide. It has helped many people isolate problem areas by explaining how to test hardware as well as software.

Troubleshooting Steps for Windows 7