I'm CC'ing the JBrowse list as people there may have additional suggestions.
My guess is that JSON.pm was not installed on the system, or if it was installed, it's in a place that is not in @INC. A common cause of this is installing JSON.pm as a regular user, rather than as root.
If you haven't already done so, please install JSON with CPAN.
Can't locate JSON.pm in @INC (@INC contains: /var/www/jbrowse/bin/../lib /etc/perl /usr/local/lib/perl/5.10.1 /usr/local/share/perl/5.10.1 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.10 /usr/share/perl/5.10 /usr/local/lib/site_perl .) at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 10.
BEGIN failed--compilation aborted at /var/www/jbrowse/bin/../lib/JsonGenerator.pm line 10.
Compilation failed in require at /var/www/jbrowse/bin/flatfile-to-json.pl line 13.
BEGIN failed--compilation aborted at /var/www/jbrowse/bin/flatfile-to-json.pl line 13.