Detecting viruses from a non-existing place?

[WhiteFlare]

I have a 320GB external hard drive that was almost full of old computer backups (pictures, docs, ect) and my current computers backup location. Since it was almost full, I went through and a lot of it was useless junk that I havnt touched or looked at for over 2 years (and most of the information is still on familys desktop sitting in the basement). So I reformatted the drive to clean it out and formated it to the new exFAT.

Now for some reason, I'm getting virus alerts coming from that clean drive to file paths that dont exist anymore.

Example:
E:\[computer name]\Backup Set 2010-08-29 190000\Backup Files 2010-08-29 190000\Backup files 3.zip

This is just 1 of the file paths out of 3 from the same drive (except coming from backup files 1 and 2.zip).

The infection is called Trojan: Java/Rowindal.A. The scan also found some Java.CVE infections coming from the backup location that does not exist.

Any ideas, I'm confused as heck.

 

[joelm3103]

What you formatted the drive with? Try using GParted and completely format the drive. Then check if that helps.

Also what AV are you using for scans?

 

[WhiteFlare]

I formated in Ubuntu Linux with gparted to FAT32 format, then formated again in Windows 7 (my main OS) with disk manager to exFAT.

I'm using an up-to-date Microsoft Security Essentials. It only seems to find things on the clean drive when I do a full scan, not a quick scan. Malwarebytes comes up clean though.

 

[joelm3103]

I formated in Ubuntu Linux with gparted to FAT32 format, then formated again in Windows 7 (my main OS) with disk manager to exFAT.

I'm using an up-to-date Microsoft Security Essentials. It only seems to find things on the clean drive when I do a full scan, not a quick scan. Malwarebytes comes up clean though.

Well I'm not totally sure why is that. When you try to clean the infection, what happens? Also you can try the guide on Spyware Asylum and see if it helped.

 

[WhiteFlare]

MSE eventually got rid of all the infections, but how they were on a clean drive in a file that no longer existed is what I'm confused about.