Backup Files Will Only Show Up If Click Show Hidden Files And Folder?

I was using my desktop like normal then an error came up saying that there was a hdd failure, and that i needed to scan for errors. all my files disappeared and only this error would come up. There would be hundreds of the same msg spamed on my screen. I scaned my hdd for errors using my Bios/Advanced options and no errors came up. I decided to take out the hdd and put it into my External Hdd bay to hook up to my laptop to extract the data off it.When i hooked it up to my laptop it showed up empty. I went into folder options and clicked on show hidden files and folders. Everything came up but it was grey/transparent. I then copied the files to another hdd for backup.

Then i formatted the hdd and put on a fresh new OS. Id like to mention i have a second internal drive that i use for backups but it wasnt backed up recently when this issue happen so i had to take out the main drive and use it as an external to back up onto another external drive.so then when i click on my second internal drive after the reinstall of the new OS it shows empty i have to go in and show hidden files and folders.. now they show again transparent. also i plug in my external to get the recent back up and all those files are still transparent when i move them to my desktop that is freshly OS installed they are still grey/transparent and i have to keep the show hidden files and folders to view them.. so its all my music, pics, documents etc they are all greyed out..i tried to copy my backup IE favs into my new IE browser and they wont show up because they are hiden it shows it copied to the favs folder but in ie i cannot view them if that makes any sense.