Hm, clearly you've done your research because something like this usually is exactly the cause of having a buffer size that's too small. Just to make sure, you are using ASIO4ALL right? ASIO4ALL is free and it's a beast of an audio driver.
Now, the cracks and pops MAY be underruns. They usually are. To check if they are, start playing something in FL Studio while having your Audio Settings window open (Options > Audio Settings) and keep an eye on your underruns count:
http://goo.gl/j4ezq
If it's increasing, then it means that there's something up with the audio driver or your computer's performance, which is weird because as you said, 2 days ago it was working fine. If it IS increasing then check this page out:
http://www.image-line.com/support/FLHelp/html/app_underrun.htm
However, like I said, those pops may not be underruns, in which case the underruns count would remain at 0. This page might provide a solution to that:
http://www.image-line.com/support/FLHelp/html/app_plugin.htm
It's unlikely that your hard disk is the problem, unless you're streaming samples directly from the hard disk with sample libraries like East/West, and even then, that would be a problem with hard disk performance and not actually filling up your hard disk with random crap.
I hope that helped. Good luck!