Those clear bodied LEDs have a very directional light output. So unless they are pointing directly at the observer, they wont appear to be very bright. But looking at them straight on, they are very bright.
The red bodied ones, emit their light in all directions.
MCD, it is measured in one point, ie. intensity. So the clear LED will have a higher number if it is measured directly in front of it.
If you were to use an integrating sphere and measure the lumens, ie, the total light output of the LED in all directions is measured, the lumen value would probably be the same for the clear and red.
Think of it as a torch with a focus-able beam. With a tight beam the light appears brighter than if it was set to light up a wide area. You have not changed the LED or the power to the LED, so lumens are the same. Just the intensity changes.
Sorry if I am teaching you to suck eggs, I used to build LEDs lights so became a bit of an LED geek!