Tracked down a bug in Text::WikiFormat with the help of Sam Vilain (mugwump). The problem was triggered because an empty regex was being used to match paragraphs, and it turns out that perlop tells us:
If the PATTERN evaluates to the empty string, the last successfully matched regular expression is used instead.
So whenever the formatter was called in a situation where a match had previously succeeded, all paragraphs were getting silently eaten. Bug report and failing test sent to chromatic, and CGI::Wiki::Formatter::UseMod 0.07 released with an interim fix.