Don't think this has anything to do with Calibre in any way. I think that there is one of two things going on. You have a spyware program that is constantly acessing your hard drive keeping an eye on what you are doing and sending that information back to the software author so that you can be targeted by adds and or so that the author can gain access to your PC and hopefully get your credit card number.
Another thing that may be happening, and is a lot less of a problem the the first posibility. Older PCs have a very slow hard drive controller (the part that actually touches the drive) and it simply can not keep up with the requests for acces to the hard drive. In this case you will need to repalce the hard drive and controller or purchase a new PC.
What do you do about the first one - install an anti-virus and anti-spyware software which will take care of the problem. Try Complete Secure at
http://completesecure.sourceforge.net/