hard drive help, it's a doosie

ok guys here's a doosie,
I have 2 hard drives one is a western digital and the other is a seagate. Until 20 minutes ago I was using the seagate hard drive because it has more space, so I was playing around with some music files, converting .Flac to
.mp3 and I noticed I couldn't erase a file even after I quit all the programs I thought could be using it so I decided to just restart my compter. So I do so and it won't make it past the black windows screen with the moving bar...it reboots itself...now i've had this problem before and I didn't really have to do anything I just started using the other hard drive and some how it eventually just started to work again...anyway i'm on the WD hard drive now and it detects the seagate one but says it's not formatted....but it is obviously. I can't run a check disk or a defrag or anything. Any advice? I don't know if this could be a factor or not but I had my ipod plugged in when I rebooted and my computer sees that as another hard drive sometimes. Any help would be awesome, thanks