If the system boots in normal mode then run the scans in normal mode.
If you use tools like MalwareBytes and ComboFix they don't need to be run in safe mode because they are designed to be run in normal mode.
Oftentimes due to malware/viruses a system isn't able to boot into safe mode as malware e.g. vundo stops the system booting into safe mode. Other nasties like sality deletes safe boot key making the system unable to into safe mode.
Run these tools and attach the logs and we'll see what they show up.
1. Download Malwarebytes' Anti-Malware to your desktop, check for the tool's Updates before running a scan.
http://www.malwarebytes.org/mbam.php
2. Please download ComboFix by sUBs:
http://download.bleepingcomputer.com/sUBs/ComboFix.exe
Now STOP all your monitoring programs (Antivirus/Antispyware, Guards and Shields) as they could easily interfere with ComboFix.
Double click combofix.exe & follow the prompts.
When finished, it will produce a log. Please save that log and attach it in your next reply.
Re-enable all the programs that were disabled during the running of ComboFix..
Note:
Do not mouse-click combofix's window while it is running. That may cause it to stall.
CF disconnects your machine from the internet. The connection is automatically restored before CF completes its run. If CF runs into difficulty and terminates prematurely, the connection can be manually restored by restarting your machine.
If needed, here's the Combofix tutorial which includes the installation of the Recovery Console:
http://www.bleepingcomputer.com/combofix/how-to-use-combofix
