Cryptsy account got hacked
I figured this out a while ago. Couple of weeks after I got hacked I noticed an unknown process in the task manager. After googling the name of the file that was linked to that process (I don't remember the file's name) I found out it was a trojan horse. Afterwards I deleted it, changed my passwords, and checked out from time to time for unfamiliar processes.
I suspect that whoever did this, connected to my accounts through my session, thus bypassing my two factor authentication both on my Cryptsy account and my Gmail.
Update:
After some digging I found an infected file named Bitcoin.Trading.Botv4.6.exe. This is probably what caused the Trojan to appear in some random temp folder. I don't remember where I downloaded this, or when I ran this, and I'm pretty sure that it wasn't identified as a threat back when I first ran it. I included a link to the scan results here.