Here is your question, rephrased (and trimmed down) as best I could decipher. Please clarify if I misunderstood, because this question is what I am answering below.

my @data = (
  'Line1 <error 1 1 <foo> <bar>> <three 1 1 <baz> <qux>> <fixv 1 1 qib
+ qeg>',
  'Line2 error 1 1 <foo> <bar> <three 1 1 <baz> <qux>> <fixv 1 1 qib q
+eg>',
); 
# The single match on Line2 is correct, 
# but I am only getting one match from Line1. 
# When I work the pattern by hand, 
# I see that it should match twice on Line2. 
# How can I get the second match?
foreach my $test (@data) { 
  if ($test =~ /(<[a-z]{4,5}\s\d\s\d\s<[^>]+?>\s<[^>]+?>>)/gx ) {
    print "Found '$1' in line '$test'\n";
  }
}
[download]

When you want to capture separate instances of the match multiple times in the same line you use the /g modifier, and either:

• loop over the match in scalar context, like while ( m/(\d+)/g ) {print $1};
• or capture all the matches at once in list context (to be looped over later), like @matches = m/(\d+)/g; .

You *cannot* refer to the second match as $2, because you only have *one* set of capturing parens in the pattern! For a simple example, see the section "More matching" in the Perl regular expressions quick start document.

Working, tested code:

use strict;
use warnings;

# Set this to 0 or 1; 
# the output will be exactly the same either way.
my $use_scalar_method = 1;

# I added the first "open inner brace", 
# so that the indentation would balance.
my $pattern = qr/
  \{           # open outer brace
    [a-z]{4,5} #   4 or 5 lowercase letters
    \s         #
    \d         #   single digit
    \s         #   
    \d         #   single digit
    \s         # 
    \{         #   open inner brace
      [^}]+?   #     everything up to the close brace
    \}         #   close inner brace
    \s         #
    \{         #   open inner brace
      [^}]+?   #     everything up to the close brace
    \}         #   close inner brace
  \}           # close outer brace
/x;
 
my @data = (
  'DataLine1 {error 1 1 {^E 0-20-9:0-50-9:0-50-9.*$} {^E 0-20-9:0-50-9
+:0-50-9.*$}} {three 1 1 {^.*35=A.*$|^.*35=5.*$} {^.*35=A.*$|^.*35=5.*
+$}} {fixv 1 1 ^.*VFIXFxProxy.*Disconnected ^.*VFIXFxProxy.*Disconnect
+ed}',
  'DataLine2 error 1 1 {^E 0-20-9:0-50-9:0-50-9.*$} {^E 0-20-9:0-50-9:
+0-50-9.*$} {three 1 1 {^.*35=A.*$|^.*35=5.*$} {^.*35=A.*$|^.*35=5.*$}
+} {fixv 1 1 ^.*VFIXFxProxy.*Disconnected ^.*VFIXFxProxy.*Disconnected
+}',
  'DataLine3 error 1 1 {^E 0-20-9:0-50-9:0-50-9.*$} {^E 0-20-9:0-50-9:
+0-50-9.*$} {twentythreeistoobig 1 1 {^.*35=A.*$|^.*35=5.*$} {^.*35=A.
+*$|^.*35=5.*$}} {fixv 1 1 ^.*VFIXFxProxy.*Disconnected ^.*VFIXFxProxy
+.*Disconnected}',
); 

my $line_number = 0;
foreach my $test (@data) { 
  $line_number++;
  print "\nLine: $line_number\n";

  if ($use_scalar_method) {
    my $match_number = 0;
    # Scalar context:
    # You can get the matches one-at-a-time this way.
    while ( $test =~ /($pattern)/g ) {
      $match_number++;
      print "Match $match_number: $1\n";
    }
    print "No matches.\n" unless $match_number;
  }
  else {
    # List context:
    # You can get all the matches at once this way.
    my @matches = ($test =~ /($pattern)/g)
      or print "No matches.\n"
      and next;
    
    my $match_number = 0;
    foreach my $match (@matches) {
      $match_number++;
      print "Match $match_number: $match\n";
    }
  }
}
[download]