Explorer has done this for over a decade. The cause is well known but the cure will have to come from Microsoft. Sorry, but unless you move videos and such off that drive we know Explorer and the Indexing does exactly what you are complaining about.
There are more reasons such as a bum install of the OS but let's hope the folk that installed it had a solid plan and didn't wing it.
I've had this problem from day 1 on my custom built computer. It's been about 3 months. Basically whenever I have any usb flash drive or my 2tb external hard drive plugged in and transferring files, playing music/movies, or playing games from it, it'll freeze up on occasion. Sometimes it'll be repeatedly, freezing up for 30 seconds, a couple times within 5 minutes. Sometimes it'll be good for quite awhile and then it freezes, and then it acts like it just got unplugged, then replugged back in. Sometimes it's consistent every 10 minutes. I also notice that it takes about 10 seconds longer for my computer to boot up (I have an ssd so it's noticeable).
I know it's not my usb ports, because my mouses/keyboards/headphones/phone cable work just fine with all the ports. I also know it's not the hard drives themselves. My 2tb is a 3.0, just an fyi. It works just fine on my laptop and any of my friends computers.
I'm thinking it's either something wrong with the OS or it's my motherboard maybe; http://www.newegg.com/Product/Product.aspx?Item=N82E16813128495
Any suggestions how to fix this would be really nice. It's annoying playing an online game and having it keep freezing up.