Hm. I don't see any problems using 5.14 either:

C:\perl5.14-64\bin>.\perl.exe \test\junk14.pl

Starting loop

End of loop
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What versions of Time::HiRes and Windows are you using?

I using Windows 7. My library version is 1.9721

Please cut&paste the output from this modified version of your script

#!/usr/bin/perl -w
use strict;
use Win32;
use Time::HiRes;

print $], "\n", $Time::HiRes::VERSION, "\n", Win32::GetOSName();

print "\nStarting loop\n";
for ( 1..1e6 ) {

   my $t3 = Time::HiRes::time();
   my $t4 = Time::HiRes::time();
   my $t5 = $t4 - $t3;

   if( $t5 <= 0 ) {
       print "\n Value negative in count: $_";
       print "\n t3: "; printf "%.6f",$t3;
       print "\n t4: "; printf "%.6f\n",$t4;
       print "\n Negative or zero value: $t5";
   }
}
print "\nEnd of loop\n";
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