Check the standard stuff...
Loose connections
Dirty connectors
Temperature (Try CPUZ's HWMonitor, it's pretty good)
Voltage
From your description it sounds like the HDD is resetting then resuming.
This could be because of loose cables or R/W errors.
The first is easy... clean the connectors and/or replace the cables
The second is more of a problem...
Try the drive in another machine, try a different drive in your machine.
Turn on SMART monitoring in your BIOS and see if you get errors.
Check your system logs... R/W errors should be noted.