Maybe I should try my hand at explaining why this works the way it does to this fellow.
mIRC is limited to it's 16 color pallette, as you should already know. What you may not be grasping is that each of the "events" that are listed above are POINTING at CTRL+K<NUMBER>.
If you choose "Action" and then click mIRC's standard GREEN color (CTRL+K 3 -- the fourth color on your pallette list at the bottom of the window), that will make "Action" green. However, you are not assigning the the color to "Action" you are assigning the control code, ctrl+k 3, to "Action"
There's a not-so-obvious reason that it works this way. mIRC's events are designed to re-color themselves dynamically. What do I mean by "dynamically" you might ask, the answer is simple. mIRC will recolor "event" lines in your windows to whatever control code you point the event at in the alt+k window.
Press alt+k, set "Action" to use the FIFTH COLOR at the bottom of the window (This would be ctrl+k4). This is usually the bright red color. Press OK.
/echo -atc action *** This line will be dynamically recolored ***
If you did this right, that line should show up with the color (control code) that you assigned to "Action".
Now press alt+k, at the top of the window, choose "Action" then pick a DIFFERENT color, maybe the 8th color (usually orange) (ctrl+k7) at the bottom of the window by left clicking on it.
Look back at the window that you did the /echo command in, that "Bright Red (ctrl+k4)" echo should now be an "Orange (ctrl+k7)" echo.
This is generally something people don't seem to realize when they write their own custom themes.
What you should be suggesting, and has likely already been suggested before, is additional color codes to use (0-99 as opposed to 0-15). This will allow it to fall in line with /echo -c, and mIRCs way of dynamically recoloring events.
The events in the Colors/Crayons dialog point at control codes, not colors. mIRC uses these to dynamically recolor it's events, and echo's that make use of the -c switch (/echo -c action Text). It's a feature.