This has been fixed. It was due to a CSS setting in /css/common.css, which means it was visible in all of the perlmonks "themes" (not including "No Theme", which has no CSS).
Note that you may need to refresh your browser-cached copy of /css/common.css to see the change.

The specific CSS code was:

div.notetext { font-size: small }
[download]

So if you decide you want to dink with the appearance of a reply when it is the displayed thread "root", use div.notetext.

Thanks for noticing this, tye.

Update: On a related note, the styling (font size setting) of the "Reputation" part of note display — that's the part that shows the ++ and -- buttons, or the current reputation if you've already voted — has been changed from a hard-coded <font size="1"> to CSS. The styling in common.css is:

div.reputation { font-size: smaller }
[download]

in case you'd like to override that in your Display Settings (or set it to something at all, if you're using No Theme).