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I just wanted to close the loop on this in case it helps somebody else.

RHEL 5 supplies booktabs v1.618. Using booktabs v1.61803 retrieved from CTAN corrected my problem, and colored rules in longtables now work correctly.

That's exactly what I was expecting.

I appreciate the sanity check... I guess now I will start comparing the current versions of the packages in question with the ones bundled with RHEL 5 and see what is needed to reproduce your results.

What am I doing wrong? The following code compiles cleanly but does not produce the desired result:

\documentclass{article}

\usepackage{longtable}
\usepackage{booktabs}
\usepackage{colortbl}

\newcommand\mytoprule{
\arrayrulecolor{red} % This seems to have no effect :(
\toprule[4.5pt ...