It is due to separation of one or more organic solvents not completely miscible in water. Some organic solvents used in cleaning chemistry are completely soluble in water. If so, there will be only one visible phase, and all the other components will be homogeneous.
By contrast, substances are said to be immiscible if in any proportion, they do not form a homogeneous phase. For example, diethyl ether is fairly soluble in water, but these two solvents are not miscible since they are not soluble in all proportions. The other components can be partially or completely soluble in the two phases. Those that are not, will settle in either the water soluble portion, or the organic solvent portion. in this case, the colorant used is soluble in the one phase, but not the other. Without the water added, the colorant was simply a dispersed colloid, but not actually dissolved.
In organic compounds, the weight percent of hydrocarbon chain often determines the compounds miscibility with water. For example, among the alcohols, ethanol has two carbon atoms and is miscible with water, whereas octanol with a C8H17 substituent is not. Octanol's immiscibility leads it to be used as a standard for partition equilibria. This is also the case with lipids; the very long carbon chains of lipids cause them to almost always be immiscible with water.
Simply either a periodic shaking is necessary or greater dilution with water can often help, unless you'll d rather switch to a product without the problem.