[Tex/LaTex] Why does using color break superscript/subscript horizontal spacing

Question

The below snippet, within an equation array environment, gives the subsequent rendering:

F\left[C^{(n-k)}_{P_{ji}}\right]

But when I add color to the snippet (using the color package) as below (adding line breaks here to facilitate legibility) in the same environment I get the subsequent bit of unpleasantness:

\color[rgb]{0.000,0.000,1.000}F\left[\color[rgb]{0.000,0.750,0.000}C
\color[rgb]{0.000,0.750,0.000}^{(n-k)}\color[rgb]{0.750,0.750,0.000}
_{P_{ji}}\color[rgb]{0.000,0.000,1.000}\right]

I get this whether or not I include the color codes for the super and subscripts prior to the ^ and _ or within the subsequent {}s.

1 Why am I getting this discrepancy?

2 Can I easily correct it in my code using these packages?

3 Is this a bug?

And here is a full document to illustrate:

\documentclass[fleqn,10pt]{article}
\newcommand\independent{\protect\mathpalette{\protect\independenT}{\perp}}
\def\independenT#1#2{\mathrel{\rlap{$#1#2$}\mkern2mu{#1#2}}}
\usepackage{color}
\usepackage{amssymb}
\usepackage{amsmath}
\usepackage[utf8]{inputenc}
\begin{document}
\begin{eqnarray}
F\left[C^{(n-k)}_{P_{ji}}\right]
\end{eqnarray}

\begin{eqnarray}\color[rgb]{0.000,0.000,1.000}F\left[\color[rgb]{0.000,0.750,0.000}C\color[rgb]{0.000,0.750,0.000}^{(n-k)}\color[rgb]{0.750,0.750,0.000}_{P_{ji}}\color[rgb]{0.000,0.000,1.000}\right]\end{eqnarray}

\end{document}

Answer 1

A \color instruction inserts an empty math formula which makes it impossible for the subscript to be attached to the preceding atom.

Use \textcolor instead, whenever possible.

\documentclass{article}
\usepackage{xcolor}
\begin{document}

\begin{equation}
F\left[C^{(n-k)}_{P_{ji}}\right]
\end{equation}

\begin{equation}
\color[rgb]{0.000,0.000,1.000}F\left[
\color[rgb]{0.000,0.750,0.000}C
^{\textcolor[rgb]{0.000,0.750,0.000}{(n-k)}}
_{\textcolor[rgb]{0.750,0.750,0.000}{P_{ji}}}
\color[rgb]{0.000,0.000,1.000}
\right]
\end{equation}

\end{document}

Never ever use eqnarray: see eqnarray vs align