So here's what I found out. I used an extension on Chrome called Alternate Player for Twitch.tv. For whatever reason, this was blocking everything. It would not register the time I watched streams, crates, giveaways or anything. Once I removed it, everything worked as it should.
@LordEmperorShinigami I have gotten a similar response like that before, only mine was by someone who was apparently having a bad day that day. Person was very rude and even less helpful. When I received an e-mail asking for feedback on the matter, I explained it all and how I felt. Whoever read it sided with me and resolved my issue.
@Threemoons Check your extensions. You may have the same issue I had. Anything that alters Twitch could be doing it. As far as I know though, BTTV and FFZ are safe to use.