That's a little hard to reproduce. But if you can change this code to show the same behaviour then we may be able to help a little more.

use warnings;
use strict;
use Devel::Timer;

search ();

sub search
{
    my $class = shift;

    my $t = Devel::Timer->new;

    $t->mark('a');
    validate_search_index ();

    $t->mark('b');
    my $target = 'some text to search some text to search some text to
+ search some text to search ';
    $target =~ /y/ for (0..10000);
   
    $t->mark('c');
    $target =~ /y/ for (0..10000);

    $t->mark('d');
    $target =~ /y/ for (0..10000);

    $t->report;
}

sub validate_search_index
{
    my $t = Devel::Timer->new;

    $t->mark(0);
    my $target = 'some text to search some text to search some text to
+ search some text to search ';
    $target =~ /y/ for (0..10000);

    $t->mark(1);
    $target =~ /y/ for (0..10000);

    $t->mark(2);
    $target =~ /y/ for (0..10000);

    $t->mark(3);
    $target =~ /y/ for (0..10000);

    $t->mark(4);
    $target =~ /y/ for (0..10000);

    $t->report;
}
[download]

Reports:

Devel::Timer Report -- Total time: 0.0153 secs
Interval  Time    Percent
----------------------------------------------
03 -> 04  0.0045  29.47%  2 -> 3
04 -> 05  0.0036  23.84%  3 -> 4
01 -> 02  0.0036  23.59%  0 -> 1
02 -> 03  0.0035  22.95%  1 -> 2
00 -> 01  0.0000   0.14%  INIT -> 0


Devel::Timer Report -- Total time: 0.0268 secs
Interval  Time    Percent
----------------------------------------------
01 -> 02  0.0195  72.63%  a -> b
02 -> 03  0.0037  13.87%  b -> c
03 -> 04  0.0036  13.37%  c -> d
00 -> 01  0.0000   0.14%  INIT -> a
[download]