For some reason every time I use Peggy’s MMF fondant I require black, dark blue and red (!) and yes they are quite a challenge initially. ( I make mind in the Kitchenaid BTW and only hand knead at the end as per below).
As Hector says, you do need more colouring to make these shades and this will throw the liquid ratio out enough to mess things up! Also the shortening ratio although small is critical to the elasticity and smoothness of the final product.
I have used both Wilton paste and Corella powder colours and have found the powder colours perform best. You do need to dissolve the powder colours in a little warm water (e.g no more than a teaspoon) otherwise they will appear grainy in your fondant, but the depth of colour is far superior to paste IMHO!
Peggy’s recipe calls for water, so to prevent dark colour fondants becoming too wet (as Hector mentioned) I melt the marshmallows with only half the required water and add the ‘powdered colour mixed in water’ during the mixing phase then hand knead in drop by drop until the colour depth required is achieved.
Also, I never start from white when making black and red. For red I melt pink marshmallows and then a tiny amount of black prior to adding the red which gives better depth.
When making black (depending on the amount I require) during initial mixing I add a tiny bit of blue then black and the hand knead in more black.
I also find that I use about 1 teaspoon extra shortening to grease my hands when kneading (we have a different kind here in Aus to that which Peggy specifies) and occasionally about 1 tablespoon extra of icing (confectioner’s) sugar if it gets sticky to keep the glossiness and texture.
I haven’t tried it but I have heard that dissolving pure cocoa powder (e.g. not drinking chocolate) in a little warm water and adding extra 1 teaspoon shortening in the intial mix gives a good brown.
Hope this helps!