When we delete or erase, does it really erase?

Heres one for ya! I made the mistake of letting someone sit at my pc while they where spending the weekend here with our family, and after almost 3 years of good pc health, yep, I got one. Pretty smart one to, undetected by all the major spyware, and virus detectors, even got by the online scanners. After a couple of weeks of just getting tired of trying to rid it, I went a head and did aback up restore, which by the way was my first, and was succesful, just the thing was, there was still the little traces of what ever it was, virus, trojan, I still do not know the difference but however, it was changing my security policies, and rendering me helpless to rid it. I got so pissed, I could have done a whole install by now. I slaved my main hard drive because I had three partitions on it, so I could get my videos and music off the drive, and once that happened, I held only one Sata 300 gig hard drive in the tower. I took and formated it first, then did a disk wipe with Acronis, then took the old Win 98 SE disk, booted from it and did an FDisk. Rebooted using the Win XP Recovery/ Repair, and did a Diskpart, Finally Fdisked and made one larg partition instead of three mediums and I had a clean install of Windows, So I thought. Now I did a memory test, Ran Bios checks, Had no disk drives, or removable drives, not even an internet cable. Believe me, I do not want to have to do this again, It Sucks. Well after getting Windows installed, We all do it,,, Back to tweaking again, this time I was only to do bare minimum, and only run Microsoft security, Explorer, and media, just to see if all the tweaking and turning off and on really made that much difference. I go to adjust my Page file, You know right after a fresh down load, it is set to system managed, NNNOOOOO!!!! Mine was set custom size and exactly how I set it. My ASUS comes with a program for over clocking, and instead of me having to install it and go do all the tweaking, I installed it, and when it started up, it was set the way I had it before all the disk erasing. I have more instances but you get the point.
My question is to the forums, how could it not have been clean, or did I clean it and this was somewhere else besides the disk drive and memory. I am so confused, I would hate to get all my stuff reinstalled and it, it being the monster reg whacker, is what I call it, resurface. How does a drive not get erased with A Swipe, A wipe, and a format to boot, and where else could it have came from?