Depending on the chosen Venue some colours are less visible than others, that's true. Just right-click the Icon (or the Instrument's entry in the list on the left) and assign any other colour you prefer. Most of the time it's sufficient to make the assigned colour a bit darker or brighter.
The good news is that MIR 3D's "Roles" will remember their colours, too. You can even apply them without changing any other parameter (just de-select them in the selection panel at the bottom of the Preset Manager).
HTH,
/Dietz - Vienna Symphonic Library