Sorry for late reply. Found out the cause of everything: LOOSE SATA CABLE. I replaced the cable since the old one had a bad design and it didn't have a tight fit.
Shortly after the last reply, my secondary hard drive, where I was having the problems, suddenly unmounted itself and kept doing this randomly after each reboot. Sometimes it would stay there for about an hour, sometimes a few days before it unmounted. I replaced the cable and I have tested everything. All is well now. I should have tested to see if the same problem occurred on a different hard drive. Oh well, lessons learned. Thank you Saltgrass for the help.