So it appears your problem is not malware, but it is inconsistent. It MAY be the HDD. But it also could be something as simple as a bad cable connection. I've seen this many times - an older machine develops oxidation in the contact surfaces in some connector, and the data signals become inconsistent. IF that is your problem, there is a simple fix you can do, just with a little care.
Disconnect your power cord and open the case. Carefully go through the entire system. At every point where a cable is plugged in somewhere, disconnect it and plug it back in again, 2 or 3 times. Do this ONE connector at a time if at all possible so you don't mix things up. The "Careful' is: make sure you don't bump something else and break it or even loosen a good connection. Doing this will cause a sort of "scrubbing" action on the contacting surfaces and clean off any thin oxidation layer. When you're done, look over the system again to be sure everything is still connected where it should be. Then close up, reconnect power and reboot.
IF this eliminates the problem you've found a solution - at least, until the next time it happens. If it does not change anything, you have to look for another cause. One thing it could be is a failing power supply OR a similar failure on the mobo itself. I don't know how old your system is. Back a few years ago there was a rash of problems with PSU's that failed early in their lifetime, and it was traced to certain batches of poor capacitors in their filter circuits. What many don't realize is that the same components and problems also showed up on mobos themselves. The symptom is bulged tops on the cylindrical capacitor cases in the PSU or in the power regulation area of the mobo.
I don't know what "disk test" system you used. Among the best, though, are ones provided free by HDD manufacturers. Most are specific to their own products. So if your HDD was made by Seagate or Maxtor, you get Seagate's Seatools for DOS; if it's WD, get their Data Lifeguard. Other makers have their own. Personally I prefer the "for DOS" versions. With them you actually write your own bootable floppy diskette or burn (from an .iso image) your own bootable CD-R disk, then you boot the machine from that. The system loads a mini-DOS into RAM and you run from there, entirely independent of the OS on your HDD, so this works even if the HDD itself is troublesome. They have a bunch of tests you can run from a menu system. Most will do NO damage to the data on your HDD, but some of the utilities included that will FIX problems for you will actually write new data, or even wipe out your whole disk! Those that are dangerous to old data will warn you fully first, so pay attention to the messages. If these utilities tell you your HDD has no hardware problems, you don't. If they say you have problems, write down the info and consult the HDD maker's Tech Support people for guidance. If there are no hardware issues but your machine still malfunctions, either you have an intermittent hardware issue that may not be disk-related, or you have a software problem.