Hello and welcome to SpywareHammer,
Your logs from DDS do not indicate any obvious Malware. Microsoft Security Essentials is flagged as your primary security application, there are however still references to McAfee Security onboard and running.
Did you previously have McAfee security installed before MSE? Two security apps running together is definitely not recommended and may very well cause the issues you mention.
I did note the following entry in Event Viewer:
6/12/2012 6:45:43 AM, Error: ACPI  - : The embedded controller (EC) did not respond within the specified timeout period. This may indicate that there is an error in the EC hardware or firmware or that the BIOS is accessing the EC incorrectly. You should check with your computer manufacturer for an upgraded BIOS. In some situations, this error may cause the computer to function incorrectly.
The first thing to do is completely remove all McAfee entries from the system then see how it responds:
and download the McAfee removal tool, save it to your Desktop
. Double click the tool to run it, Vista or Windows 7 users right click and select "Run as Administrator" re-boot when requested to complete the task.
See how the system responds after removing McAfee..