Ok, so I found out that it is mold. At least in my top tray.
As you can see from the picture my system is close to the fireplace so there shouldn't be any humidity around. The drainage holes have been opened double what they used to be. The temp upstairs right now is 74F and downstairs its around 55ish.
This is what my trays look like. I would think there was plenty of drainage.
I've been trying to keep an eye on it everyday now and the top tray has the beginning starts of mold. Little black specs and a faint smell. My phone won't take a good enough picture of it so I can show it. I'm going to completely clean absolutely everything from the pump to the trays to what holds the water today.