Yes, it should be caused by virus. Did you format your USB? If you did not, check whether the folders are not in hidden mode. Please follow those steps. Hope this hleps.
Firstly:
Download "AutorunExterminator" from Cnet http://download.cnet.com/AutorunExterminator/3000-2239_4-10912924.html Extract it --> Double-click on "AutorunExterminator" --> Plug your USB drive now. It will help remove the autorun.inf files from both your usb and the drives.
Secondly:
Click on "Start" -->Run --> type cmd and click on OK.
Here I assume your usb letter as G:
Enter this command.
attrib -h -r -s /s /d g:\*.*
You can copy the above command --> Right-click in the Command Prompt and paste it.
Note : Don't forget to replace the letter g with your pen drive letter.
Press Enter
Now check for your files in Pen Drive.
Thirdly:
After that, download the Malwarebytes' Anti-Malware from CNET http://download.cnet.com/Malwarebytes-Anti-Malware/3000-8022_4-10804572.html
Update it --> Perform "Full Scan" (Note : Default selected option is "Quick Scan")
Open run and open cmd
type this cod: attrib -h -r -s /s /d g:\*.*
notic:"g" is your drive
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