First off, you really want to avoid any dark colored (or even moderate colored) juices in the eGo-T / Tornado-T / Inferno-T. They gunk up in this design, and cause many problems with your tankomizers.
Second, I have noticed the same thing when I said "screw it" and tried one of my dark juices. It also seemed that the dark area was a lot thicker than the surrounding juice. I believed this was caused by over-vaping, and the needle heating up the juice to the point of "cooking" it, causing it to thicken and darken. This lead me to believe that I either needed to take more time between vapes on the dark juice, or stop using it in the Tank. I took the second option, as I chain vape, and hate waiting between puffs.
If you stay with the dark juice, you will need to undertake severe cleaning regimens
I have plenty of tricks and tips on cleaning and maintenance on my blog. Link is in my signature.