Thanks Anon, I had warnings on, the $line I mentioned is actually being pulled in from a file, so no quotes are actually around it. The debug thing is a great help though!

Aha. That is why its important (as How (Not) To Ask A Question would say) to clean your room, which is also part of How do I post a question effectively?

#!/usr/bin/perl --
use strict;
use warnings;
use Test::More qw' no_plan ';

Main( @ARGV );
exit( 0 );

sub Main {
    my $line = q[F:\MF\BR\PreparedSources\acdv\test_dev\BeanName\Sessi
+onBean.RMWAppException.java];
    my $olin = q[JAVAFILE "test_dev\BeanName\SessionBean.RMWAppExcepti
+on.java" "acdv" "##All"];
    is( $line, $line, '$line is $line, duh ');
#~ http://perlmonks.com/?abspart=1;displaytype=displaycode;node_id=913
+631;part=1
    {
        use re 'debug';
        $line=~ s/^(f:\\MF\\BR\\PreparedSources\\)([a-z]+\\)([a-z]+_de
+v)(\\)([a-z]+)(.java)$/JAVAFILE "$4$5$6" "$2" "##All"/;
    }
    is( $line, $olin, '$line is $olin');
    $line=~ s~
    ^ # anchor start of line
    ( # $1 # f:\MF\BR\PreparedSources\
        [^\\\/]+[\\\/] # f:\
        [^\\\/]+[\\\/] # MF\
        [^\\\/]+[\\\/] # BR\
        [^\\\/]+[\\\/] # PreparedSources\
    )
    ( # $2  # acdv
        [^\\\/]+
    )
    [\\\/] 
    ( # $3 # test_dev
        [^\\\/]+?_dev
    )
    ( # $4 # \BeanName\SessionBean.RMWAppException.java
        [\\\/]
        .+ 
        (?i-xsm:\.java)
    )
    $ ## anchor end of line
    ~JAVAFILE "$3$4" "$2" "##All"~x;
    # //x means whitespace is insignificant
    is( $line, $olin, '$line is $olin for real');
}
__END__
Compiling REx "^(f:\\MF\\BR\\PreparedSources\\)([a-z]+\\)([a-z]+_dev)(
+\\)(["...
Final program:
   1: BOL (2)
   2: OPEN1 (4)
   4:   EXACT <f:\\MF\\BR\\PreparedSources\\> (12)
  12: CLOSE1 (14)
  14: OPEN2 (16)
  16:   PLUS (28)
  17:     ANYOF[a-z][] (0)
  28:   EXACT <\\> (30)
  30: CLOSE2 (32)
  32: OPEN3 (34)
  34:   PLUS (46)
  35:     ANYOF[a-z][] (0)
  46:   EXACT <_dev> (48)
  48: CLOSE3 (50)
  50: OPEN4 (52)
  52:   EXACT <\\> (54)
  54: CLOSE4 (56)
  56: OPEN5 (58)
  58:   PLUS (70)
  59:     ANYOF[a-z][] (0)
  70: CLOSE5 (72)
  72: OPEN6 (74)
  74:   REG_ANY (75)
  75:   EXACT <java> (77)
  77: CLOSE6 (79)
  79: EOL (80)
  80: END (0)
anchored "f:\MF\BR\PreparedSources\" at 0 floating "_dev\" at 28..2147
+483647 (checking anchored) anchored(BOL) minlen 39
ok 1 - $line is $line, duh
Guessing start of match in sv for REx "^(f:\\MF\\BR\\PreparedSources\\
+)([a-z]+\\)([a-z]+_dev)(\\)(["... against "F:\MF\BR\PreparedSources\a
+cdv\test_dev\BeanName\SessionBean."...
String not equal...
Match rejected by optimizer
not ok 2 - $line is $olin
#   Failed test '$line is $olin'
#   at D:\dev\misc\pm.913631.pl line 25.
#          got: 'F:\MF\BR\PreparedSources\acdv\test_dev\BeanName\Sessi
+onBean.RMWAppException.java'
#     expected: 'JAVAFILE "test_dev\BeanName\SessionBean.RMWAppExcepti
+on.java" "acdv" "##All"'
ok 3 - $line is $olin for real
1..3
# Looks like you failed 1 test of 3.
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