<pre> tags are four points smaller than <code> tags

Sounds like a (personal?) CSS problem. For reference, the following are the same size for me in this browser:

Pre tags are THIS big

Code tags are THIS big
[download]

I haven't changed my site display CSS (except for blocking a couple trolls) and the pre is much larger than the code in Firefox and Safari on OS X. Gotta love HTML. The font size below is the culprit, I think-

<pre>Pre tags are THIS big </pre>
<pre class="code">
  <div class="codeblock">
    <tt class="codetext">
      <font size="-1">Code tags are THIS big </font>
    </tt>
  </div>
[download]

Update/amendment: they do display the same threaded beneath the OP but not when viewed singly.

the pre is much larger than the code

That's because you haven't turned on the "Large Code Font" option in Display Settings. The <font size="-1"> was added (a long, long time ago...) because (due to tradition and stupidity) font sizes are mostly specified only according to height which means that a fixed-width font of the "same size" can look quite a bit larger than a variable-width font. So it could make code blocks rather dominant a node. So code blocks had their size decreased slightly. But that made code hard to read in some situations so this slight shrinkage was made optional.

Note that work that is currently mostly being done by jdporter will eventually replace the <font size="-1"> with some CSS and we know (based on previous work done by Petruchio) that this will also cause the perceived size of things to change (in inconsistent ways that will vary even based on what fonts a person has installed). But it will also make it easier for visitors to use CSS to control the sizes of fonts here so we'll put up with the inevitable period of adjustment eventually.

- tye