Wait, wait.. you use Spybot and MalwareBytes?
How many anti-virus and related programs do you have installed?
They have been known to fight one another and render one another useless. Best situation = one all-in-one solution installed, nothing else installed.
Potentially handy links:
http://forums.pcworld.com/index.php?/to ... safe-mode/
There's also Comodo, which I have heard good things about. At any rate, it sounds like you probably COULD stand a good reinstall of Windows. Reinstall and choose one good anti-virus. Avast! paid editions have a command line scanner as mentioned in the second link above, which can work in safe mode. Safe mode in Windows really isn't that hot a deal, though, at least not for normality. You can foul up Windows just as easily in safe mode as a normal boot. It depends on your habits and how up-to-date everything is. It's akin to putting on a safety helmet when one might already be riding atop a raging fast Wile E. Coyote contraption fueled by dangerously amateur rockets. It's really not going to offer much protection in many situations. If you don't feel safe enough using Windows in normal mode, there's probably much bigger problems going on that need to be dealt with, anyway. An infected computer is still infected even in safe mode.
Also, check this out:
http://www.pcadvisor.co.uk/features/sec ... cting-you/
Some people will try to tell you that it is ok to have more than one anti-virus installed as long as no more than one of them is set to do realtime scans. This is fundamentally inaccurate. It doesn't make sense to have more than one antivirus installed, even if only one of them does realtime scans. It's unnecessary and computers do not do unnecessary well, especially concerning critical security areas. Give them any chance to identify a competing AV program as a security threat and they'll try to do something about it. It might not be noticeable, but it is almost assured that something will get mucked up and rendered useless.
AV 1: Hey, kid.. why are you rooting around in my root? You're a virus, aren't you? Sorry, I cannot let you proceed. Papers, please.
AV 2: Hey, kid.. why are you rooting around in my root asking for papers? You're a virus, aren't you? Sorry, I cannot let you proceed. Papers, please.
AV 1: You're asking for MY credentials?! You're a spy, aren't you?! Well, see how you like this!
AV 2: Hey, I needed that! You're a spy, aren't you? Well, take this!
AV 1: I knew it! What are you, KGB? JCB? Interpol?! Tell me who sent you!
AV 2: I knew it! What are you, CIA? G2? 8200?! Tell me who sent you!