Using LDR and RGB Led to get R,G,B values
Your are probably doing the white calibration with some clear liquid,
like water. The LDR is then lit directly by the LEDs, and is getting too
much light. It's resistance is then very low compared to the pull-down
resistor in series with it. You end up measuring something very close to
5&nbsp;V.

You should try to reduce the amount of light hitting the LDR. A neutral
density filter (the kind used in photography) would be ideal.
Alternatively, you could increase the distance between the LEDs and the
LDR, and put some translucent paper in between. You could also add a
diaphragm (a small hole). Then, you can also lower the resistance of the
pull-down in order to get lower voltage readings, but beware not to draw
too much current.

A comment about the instructable you linked to: owing to the highly
non-linear characteristic of the readings you get, it is quite likely
that you get unequal RGB vales from a neutral grey. Some kind of
linearization (estimating actual light fluxes) would be needed if you
want neutral greys to be measured as neutral greys.