I'm not 100% sold that it's virus related but I have this guide in case. It also wouldn't hurt to format your flash drive too.
There are a few better things to do. (This does not come with a warranty, you are responsible for any software issues caused by running any of these scans.) That being said, I work at an MSP and use these tools daily.
1) Download and run rkill: http://www.bleepingcomputer.com/download/rkill//dl/10/
2) Download and run MalwareBytes (note, do not install pro): http://www.bleepingcomputer.com/download/malwarebytes-anti-malware/dl/7/
3) Download and run combofix (note, you will lose internet connection): http://www.bleepingcomputer.com/download/combofix/
4) Download and run rootkit remover:
http://downloadcenter.mcafee.com/products/mcafee-avert/rr/rootkitremover.exe
5) Download and run Kaspersky Virus Removal Tool:
http://devbuilds.kaspersky-labs.com/devbuilds/AVPTool/avptool11/setup_11.0.0.1245.x01_2013_06_07_22_58.exe
6): Install your preferred AV software: I use AVG or Microsoft Security Essentials for personal computers and Kaspersky for work PC's. Also, remember “There is only one Lord of the Ring, only one who can bend it to his will. And he does not share power. –Gandalf.” He was also talking about anti-virus software too. DO NOT INSTALL MULTIPLE COPIES OF ANTI-VIRUS SOFTWARE!!!
Good luck and let us know what you catch.