... why the + after the first set of parens?

Because I made a mistake and didn't notice because I was getting the right results. It is redundant and removing it makes no difference--'cept maybe it'll run a insy winsy bit quicker? :)

There is a second 'artifact' in the replacement. ($1||'') can become just $1.

I was attempting to avoid the need to suppress warnings, but it turns the code it a mess of bracketed ||s and ternaries; or a long if then else chain. Warnings are optional and turning them off, as an informed decision to avoid complicated code, is (IMO) legit. So I chose the cleaner option. You can replace local $^W; with no warnings 'uninitialised'; or the chain of defined and length tests if you prefer.

Does this explain it?

#! perl -slw
use strict;

while( <DATA> ) {
    chomp;
    printf "Before '%s' becomes ", $_;
    s[
        ( \d+ )             ## Grab any digits before a decimal point
        (?:
            \.              ## If there is a decimal point
            ( \d{0,2} )     ## Try grab two digits after it
            ( \d* )         ## And any more into another capture
        )?                  ## All conditionally
        %                   ## And finally...
    ]{
        local $^W;          ## I know some of the captures will be emp
+ty.

        ## Pad (trailing zeros) the digits being moved to ensure exact
+ly 2
        my $n = substr( $2 . '00', 0, 2 );

        ## Reassemble the number from 
        ##      Any digits previously before the decimal point
        ##      The two digits being moved
        ##      A decimal point and the remaining digits if there are 
+any.
        $1 . $n . ( length($3) ? ".$3" : '' );
    }xe;
    print "'$_'";
}

__DATA__
[download]