while (<ACTLIST>)
    {
        $TheLine = $_;
        @WordList = "$TheLine";
    }
[download]

Try this instead:

   while (<ACTLIST>)
    {
        push @WordList, $_;
    }
[download]

@WordList = (<ACTLIST>);
[download]

Gary Blackburn
Trained Killer

1. put 'use strict;' and 'use warnings;' at the top of your script. This will require you to declare all your variables using my or our. (Use my unless you know you need to use our. If you don't understand, just use my.)
2. The following works just fine:

   while (my $theLine = <INPUT>) {
   [download]

   And, it will even make sure that you kick out of the while loop when the file is empty.
3. Use consistent block formatting. That will help you catch logic errors. For example, your second while-loop could look like:

   while (my $TheLine = <INPUT>)
   {
       if ($TheLine =~ /<RD>[^\n]*Status Compendium<<.JL>/i)
       {
           my $ListPos = 0;
           until($ListPos > $#WordList)
           {
               if ($TheLine eq $WordList[$ListPos])
               {
                   $TheLine = "";
                   pop(@WordList)
               }
   
               $ListPos +=1
           }
       }
       print OUTPUT "$TheLine";
   }
   [download]

Also - read up on pop. I don't think it does what you think it does.

------
We are the carpenters and bricklayers of the Information Age.

Don't go borrowing trouble. For programmers, this means Worry only about what you need to implement.

A few more things:

1. First off, after you use strict; like dragonchild recommended, you will notice that @WordList isn't scoped properly. Also, while you have the right idea towards good, modular code by using functions, your functions need to be... functionized. The first one, actsin1, doesn't even really need to be a function at all. In fact, if it wasn't a function, you would no longer have any scoping problems associated with @WordList. Your The second one, Group, should accept the array as an argument. Keeping a tight scope is a good programming practice.
2. $ListPos +=1 should be $ListPos++. Its much more readable this way - the ++ operator is there for a reason, you know :)
3. In your file paths, just use a single forward slash - perl will translate the slashes to the correct type based on the system.
4. This block:
   

            if ($TheLine =~ /<RD>[^\n]*Status Compendium<<.JL>/i)
           {
                   $ListPos = 0;
                   until($ListPos > $#WordList)
                   {
                       if ($TheLine eq $WordList[$ListPos])
                       {
                           $TheLine = "";
                              pop(@WordList)
                       }
                   $ListPos +=1
                   }
                  }
           print OUTPUT "$TheLine";
   [download]

   can be reduced to:
   

   if ($TheLine =~ /<RD>[^\n]*Status Compendium<<.JL>/i)
   {
        for(my $i=0; $i > @WordList; $i++)
        {
             print OUTPUT $TheLine if ($TheLine ne $WordList[$i])
        }
   }
   [download]

   
   This is much more easy to read and efficient, since you arent using @WordList after you are done with the program. Give it a whirl.
5. Instead of explictly timing your program, consider using Benchmark. It is much more accurate

Sorry for being nitpicky, but I felt the urge :) Good Luck!

#4 can be reduced to a hash, which is shorter and more efficient yet. Besides that, I doubt the OP wants to print $TheLine for each word it doesn't match.

Thanks for the help, when I made the changes and ran the script it hangs and returns a null file newstat.fff after about 5 mins. The Statutes.fff file is 400mb. What I am attempting to do is relpace words in the main file from a list of words in a text file (each word is seperated by a line break). I want the output to be a new file which contains all the old text minus the words not wanted.