Virus, or faulty USB drive?

I plugged in my USB drive into my Macbook Pro and it suddenly disconnected while I was renaming a folder. When I plugged it back in, I realised a large chunk of my files were gone, and I had a whole bunch of files with jumbled letters as their name in my USB pendrive. I checked and they were "Alias" files it seems.
Is this a sign of a virus, or is the problem my USB pendrive?

That's not a virus. Disconnecting any drive unexpectedly has the potential to cause problems, including corruption of the drive and subsequent data loss. Try repairing the drive using Disk Utility (found in the Utilities folder in the Applications folder).
If that doesn't work, do you have the files on that drive backed up anywhere? If not, you may be about to learn the hard way why backups are important. Try recovering what files you can using Data Rescue 3.

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    I've tried removing iTunes several times and ensuring that all remnants of the installation are gone (registry and folders on the installation drive) and have disconnected all my USB devices short of the keyboard and mouse and still I get the same results. At this point, I'm afraid that a re-install of Windows is going to be the solution; but it's a drastic one (I have a SSD drive where Windows is installed along with all of my games for faster load times/better performance and do not want to have to redownload\reinstall all of them) and I'm not prepared to undertake it at this time, which is why I'm posting here
    I've used a utility called USBDeview that sees my phone is connected - so I know from a functional standpoint that my USB ports are good and working. I also know the cable is good too - my daughter's PC (Windows 7 32-bit with NO iTunes) immediately sees the device when I plug it in, installs the drivers, recognizes it as an iPhone and I can then see/browse it in Windows Explorer like I would normally expect. My work PC (Windows 7 64bit, NO iTunes) sees the device just fine as well. I would immensely appreciate anyone that has seen this issue or has any additional solutions I can try.
    It's also worth mentioning that I've never used Kapersky antivirus so the UPPERFILTERS value in the registry that I've seen as a solution on some forums is not present on my machine. I'm using Microsoft Security Essentials as my antivirus (no flaming please lol - it meets my needs and is extremely lightweight, which is why I'm using it on a gaming rig) and it's not indicating any issues. I've also tried running iTunes as an administrator (even though my account is a local admin on the machine) and that does not have any effect either.
    If there is anything I left out, please let me know; and I thank you in advance!

    AphexTwin wrote:
    - no Apple input?
    Of course not.  Didn't you bother to read the TOU of this forum?  This is a USER TO USER technical support forum.  Apple doesn't post here.

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