If the version of LWP::UserAgent that was installed does something differently then the version of UserAgent you originally used, the answer is, yes, it could have broken something. However, I've noticed you don't have:

use strict;
use warnings;
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At the top of your script. So I ran your script and added those two lines and got the following:

Global symbol "@lines" requires explicit package name at - l
+ine 8.
Global symbol "$out" requires explicit package name at - lin
+e 10.
Global symbol "@lines" requires explicit package name at - l
+ine 10.
Global symbol "@lines" requires explicit package name at - l
+ine 12.
BEGIN not safe after errors--compilation aborted at - line 13.
[Fri Feb 13 01:48:06 2004] -: Global symbol "@lines" requires explicit
+ package name at - line 8.
[Fri Feb 13 01:48:06 2004] -: Global symbol "$out" requires explicit p
+ackage name at - line 10.
[Fri Feb 13 01:48:06 2004] -: Global symbol "@lines" requires explicit
+ package name at - line 10.
[Fri Feb 13 01:48:06 2004] -: Global symbol "@lines" requires explicit
+ package name at - line 12.
[Fri Feb 13 01:48:06 2004] -: BEGIN not safe after errors--compilation
+ aborted at - line 13.
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Now all those errors mean that you're not declaring before using, or that you're not explicitely accessing (i.e. Package::sub instead of sub), and this isn't necessarily the source of your errors. But it's very good practice to use warnings; use strict; at the top of your code because it helps unmask errors.

I would recommend taking the time to go through your script to make it compatible with use strict; use warnings; That may help isolate the problem.

Update: I was thinking about it, and you can compact the following lines of code:

$request = HTTP::Request->new('GET', 'http://www.bom.gov.au/cgi-bin/wr
+ap_fwo.pl?IDS10034.txt');
$res = $ua->request($request);
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Into:

my $request = $user_agent->get('http://www.bom.gov.au/cgi-bin/wrap_fwo
+.pl?IDS10034.txt');
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And not to nit pick, but you should always double check your content type. Otherwise you might accidently get a JPEG or something, i.e.:

if ($res->is_error) {
  $str = $res->message;
} else {
  $str = $res->content;
}
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Under my example would become:

if ($response->is_success 
    and ($response->content_type eq 'text/html')) {
  $str = $response->content;
}
else {
  $str = "Content type was $response->content_type"
     unless ($response->content_type eq 'text/html');
  $str = $response->status_line
     unless ($response->is_success);
}
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Of course, the updates were stylistic and a matter of preference (except for checking content type unless you are absolutely sure you can only get the proper content type). TMTOWTDI