Have a look at the mod_perl_traps perldoc file that is included with mod_perl. There are some hints at what might be going on here. From the docs:

"Use of uninitialized value"
           Because of eval context, you may see warnings with useless 
+filename/line, example:

            Use of uninitialized value at (eval 80) line 12.
            Use of uninitialized value at (eval 80) line 43.
            Use of uninitialized value at (eval 80) line 44.

           To track down where this eval is really happening, try usin
+g a __WARN__ handler to give you a stack trace:

            use Carp ();
            local $SIG{__WARN__} = \&Carp::cluck;
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It is surprising that Apache::Registry is having issues with eval'ing your CGI script though, since with CGI::Application your script is so minimal... Do you have anything more complex than the following in your cgi script:

use WebApp;
my $webapp = WebApp->new();
$webapp->run();
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Or are you doing your own eval'ing in your modules?