I've been having some issues relating to two of my harddrives...

As mentioned at the bottom of my post with my specs, I use the 40gb SSD for boot and primary applications and the Caviar Black 1tb (I haven't re-installed the second one yet I'm lazy) for everything else, ie files I am using, programs that take up huge quantities of disk space, etc.
The other day I noticed that my downloads in jDownloader had stopped and after checking for the error noticed I had 0kb free on my 1tb harddrive. How I filled up over 100gb in less than a day still confuses me as I can't find many "big" files/stuff to delete and get back to over 100+gb free. I may end up having to go through each and every folder on it to see what the **** is taking up so much room, but to my knowledge there is no where near 1tb of data on it (that I knowingly want on it...).
That aside, my main problem just happened (and may or may not be related to that problem I just mentioned): Something just ate up all my free harddrive space on my boot drive within the last hour (I know I had at least 2gb free on it). At 0kb free on the boot drive, every single application I had open crashed. I was using Compressor to convert some videos (on the 1tb harddrive) and also downloading some video (~5gb total) through jDownloader to the 1tb harddrive. I also had a few other programs open (but only idle) which were Firefox, Chrome, iTunes, Quicktime 7, Word, and Excel.
After quitting everything and rebooting etc I only have 89mb free on my boot harddrive...the other day I am positive there was over 2gb on it! I have not installed anything on it in last few weeks and nothing is stored on it besides the occasional desktop document for easy access; everything else goes to the 1tb drive. I tried looking for stuff to delete on the 40gb SSD but I honestly have no idea what just consumed all my remaining free space; I have nothing on there but applications and application data so I have no idea where to even look for stuff to delete.
Any help here as to why on two separate harddrives Ive zeroed out my free space on two separate occasions? Is it something I may be doing without knowing it? Is there something messed up with my computer?
EDIT: 5 minutes after posting this I found 700mb of store iTunes album artwork which I deleted. This had obviously been there for weeks so I know it was not the "problem" in taking up all the free space, but I DID however notice that over the next couple of minutes I lost anywhere from 10-20mb in free space on the drive. Only applications running: firefox (which I relaunched 10 min ago), little snitch (currently disabled), and last.fm audioscrobble (idle).
WHY AM I LOSING ALL THIS SPACE ON MY TWO HARDDRIVES? I have nothing left to delete to keep freeing space up!
EDIT #2: Correction: over last 5 or so minutes the free space on my harddrive has dropped from 690mb to 657mb.
Message was edited by: Tnglen
Message was edited by: Tnglen

When the story gets long, helps to have a short summary and bullet points.
SSD: do not zero - hope you checked into that first. AT this point, you need to reformat and restore it. And 40GB may be on the small size.
No matter what you do, the system drive does a lot of work also all the time with temp files, paging etc.
Zero - some minimal value before partitioning, I don't see any for doing so to free space. And it has to lock all the space to do its operations.
Even on an SSD, but for any drive and boot volume more so, keep 10GB or 10% (larger of the two) of free space minimum.
There are a number of threads and help on vanishing free space in "Using Mac OS X Snow Leopard"
I suggest booting from another hard drive and running DU First Aid at a minimum.
Look at your drive with OmniDiskSweeper to see what and where.
The BEST tool for formatting drives and SSDs would be SoftRAID bar none, and especially for setting up a drive to begin with.
http://www.softraid.com - check features and the pdf guides
Use your 4-5 drive bays, system, scratch and editing, media files, user data, and one for backup (not a fan of TimeMachine but of cloned volumes).

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