Hiya mate,
I wouldn't want to speculate too much about the reason, as the Trojan on its own shouldn't clear vast swathes of disk; but then there might be something else so far undetected in there too, or if other 'safe' files are becoming infected by malware, they might be being deleted by security software because of their infection, but of course breaking the apps that depend on them.
I doubt it's a hardware issue whatever has happened. You could get issues like you've described attributable to memory failure, or flawed drivers/runtimes, but the fact you've noticed a large amount of free space appearing would indicate something has, or is still, going wrong with software.
Anyway, to the resolve - I'd be more inclined to level it and start again - after all, reinstalling things one by one could be pretty labour intensive, you might not get everything fixed, and there's a large chance whatever has caused it will still be present and may simply lead to it all happening again.
I'd format and reisntall, and make sure one of the first apps installed after doing that is a decent security app. We can all debate which one's best for hours, they all have good and bad points. All I'll say is that I run Symantec Anti-Virus Corporate Edition, it's got none of the 'Norton Nonsense' and has an improved heuristics engine. It sits quietly in the system tray doing its thing, never nags about anything, and only really ever shows itself when it has actioned a risk. It's extremely effective at stoppings virii getting in, and most malware that isn't by definition a virus is also prevented. In short, it's great. It's expensive to buy but there are ways around that.
Just one thing to note, if you are going to 'research' getting SAV Corp; install something to protect you while you do so - even if it's only AVG, it's better than nothing, but I wouldn't rely on that long-term. We did some extensive testing into different security solutions and following that research AVG will forever be known to my colleagues and I as 'Fisher Price My First Anti-Virus'.
Using SAV Corp and updated Firefox has prevented anything the internet has ever tried to throw at me getting in. For Firewall I use Comodo Firewall Pro (free version) - since Sygate is no longer available this is probably the best free Firewall out there, very configurable and great for folks at all levels of technical prowess. Comodo also includes some malware prevention built-in in the form of 'Defense+' but to be honest while I've got SAV Corp installed I just turn that off.
If you're leeching stuff from Torrents you need to think about getting yourself a Giganews subscription, a copy of Newsbin Pro and a subscribtion at Newzbin for reports - you get everything A LOT faster (in terms of release date and download speed), don't run the risk of being in the doo-doo for uploading, and it tends to be a LOT safer in terms of security as an almost insignificant fraction of binaries are infected when comparing with the stuff that goes out via Torrent. The only down-side is it will cost you up to £20 a month - but it pays for itself VERY quickly...
Regards,
Rob.
