Close (and I do understand needing caffeine before coding) but Re: failure to generate report file doesn't deal with OP's request to capture only those with 3600 second separation. Others, however, have dealt with that.

But (and as OP replied) $seen is used only once in your code. Minor mods correct that issue (and ignore the count):

#!/usr/bin/perl -w

open In, "log.2008-01-11" or die "log: $!\n";
open Out, ">report.2008-01-11.txt" or die "report: $!\n";
while (<In>){
    chomp;
    next unless ($_ =~/channel = two.* (\d+)$/);
    print Out "$_  \n";
}
close In;
close Out;
[download]

produces

2007-Jan-11 00:00:01 UTC (GMT +0000) - Poll: channel = two, ref = com,
+ id = 133714761  
2007-Jan-11 00:00:01 UTC (GMT +0000) - Poll: channel = two, ref = com,
+ id = 595131400  
2007-Jan-11 00:00:02 UTC (GMT +0000) - Poll: channel = two, ref = com,
+ id = 595191883  
2007-Jan-11 00:00:04 UTC (GMT +0000) - Poll: channel = two, ref = com,
+ id = 006456768  
2007-Jan-11 01:07:06 UTC (GMT +0000) - Poll: channel = two, ref = com,
+ id = 133714761
[download]