If I understand your complaint, scripts that formerly sent fatal errors to STDOUT with mark-up now send fatal errors to STDERR.
Another monk gave you a good piece of advice: run the program from the command line. If you see something like the output from the one-liner included below, then you'll know that CGI::Carp is doing what it's supposed to. If not, then something is probably broken somewhere (how helpful is that?!).
Have any of the modules you're using been been upgraded recently? What about perl? Have there been any changes to the server software or configuration? Are there other users you could check with to see if they're experiencing the same problem?
$ perl -Mstrict -wle 'use CGI qw/:standard/; use CGI::Carp qw/fatalsTo
+Browser/; print header, h1("hello"); $test = 1'
<PRE>Global symbol "$test" requires explicit package name at
+ -e line 1.
Execution of -e aborted due to compilation errors.
For help, please send mail to this site's webmaster, giving this error
and the time and date of the error.
[Wed Dec 12 10:44:45 2001] -e: Global symbol "$test" requires explicit
+ package name at -e line 1.
[Wed Dec 12 10:44:45 2001] -e: Execution of -e aborted due to compilat