My first step would be to go to the website of your hard drive's manufacturer. Find there and download for free their disk diagnostic utilities package. Seagate has their Seatools for DOS or Windows, WD has Data Lifegard, etc. If you can, download (on another machine if your can't work) the version that has you burn your own diagnostic disk on a CD-R. Then you boot your machine from your optical drive with this disk. It will load a mini-DOS into RAM and you can run all its diagnostics on your hard drive(s) completely independent of Windows. It may find disk problems it can fix, it may find no problems at all, or it may tell you you have significant HDD faults. In the last case, contact Tech Support for your HDD and tell them exactly what the diagnostics say so they can arrange a fix or replacement.
For something as intermittent as you describe it is unlikely the problem is in BIOS Setup configuration. If you find no HDD errors with the diagnostic tests, then you will know to concentrate on Windows software issues and / or hardware problems like loose or defective cables.