It seems adding a single line fixes the issue:

Line to add:
---------------------
$result = floatval($result . ' ');


Working version:
---------------------
$value1 = '1';
$value2 = '0.9';
$value3 = 0.1;

$result = floatval(floatval($value1) - floatval($value2));

$result = floatval($result . ' ');

if ($result >= $value3)
{
	echo 'Working as intended';
}
else
{
	echo "$result IS NOT >= $value3<br />";
	var_dump($result, $value3);
}

Floating point values have a limited precision. Hence a value might 
not have the same string representation after any processing. That also
includes writing a floating point value in your script and directly 
printing it without any mathematical operations.

If you would like to know more about "floats" and what IEEE
754 is, read this:
http://docs.sun.com/source/806-3568/ncg_goldberg.html
 
Thank you for your interest in PHP.

.

$v = 'string';
$f = floatval($v);
if ($f == $v) {
    echo "$f == $v" . PHP_EOL;
} else {
    echo 'not equals' . PHP_EOL;
}