It's pretty common and totally normal for the clutch fluid to darken/blacken, especially when components are replaced. The new master and slave cylinders are honed with a crosshatch pattern to aid in sealing, and low stiction. The crosshatching in the steel acts like a micro cheese grater on the rubber seals.
If you think about the distance the seals travel along that scored surface each time the clutch is cycled, and how often they get cycled back and forth while driving, it doesn't take long for the fluid to turn dark or black, contaminated with lots of microscopic particles of rubber. Once the rubber is suspended in the fluid, the back and forth motion of fluid through the system pushes it up into the master, where it can settle and stick to every available surface in the reservoir, making the fluid in the cup appear even darker.
Once everything is broken in, you should be able to flush it and have the darkening process take much longer, but it will still happen.
If it's not leaking anywhere, but it's not holding pressure, you may have air in the line. Also, check the condition of the rubber hose to make sure it's not expanding when you hold the clutch.
- Josh