The color difference can really vary depending on the monitor you have, especially between CRT and LCD, and in the case of an LCD monitor, your viewing angle to your monitor. For example on both of my laptops (MacBook Pro and Dell), I certainly wouldn't call that 'ever-so-slightly-darker'; it's quite obviously a different shade than the background.
I did find the region of CSS though. Both in meta and in the main site, code blocks have a deliberate background of #eee: (the following snippet is identical in both CSS files)
code{font-family:Consolas, Menlo, Monaco, Lucida Console, Liberation Mono, DejaVu Sans Mono, Bitstream Vera Sans Mono, Courier New, monospace, serif;color:#222;background-color:#eee;}
I'd label it as a feature. I like how it makes the code block stand out, and I think that's the point.