It's often helpful if you can give a runnable sample of you code that exhibits the problem. The following is based on your sample and runs as expected on my system:

use strict;
use warnings;

use Tk;
use Win32::Clipboard;
use Win32::Process;
$::CLIP = Win32::Clipboard();


my $ProcessObj;

Win32::Process::Create($ProcessObj,
        'c:\Windows\system32\notepad.exe',
        "notepad",
        0,
        NORMAL_PRIORITY_CLASS,
        ".")
    || die "Can't create";

my $emptytries = 0;
my $clip;
while (1)
{
    $clip = Win32::Clipboard::GetText();
    if ($clip)
    {
        print "$clip\n\n";
        $::CLIP->Empty();
        $emptytries = 0;
        sleep(5);
    }
    else
    {
        $emptytries++;
        last if ($emptytries >= 3);
        print ".";
        sleep(1);
    }
}

$ProcessObj->Wait(INFINITE);

print "Done";
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Prints:

asddf

..Done
[download]