Ваще без jQuery

<fieldset data-role="controlgroup" id="timer_t_ur">
				<legend>Интервалы работы долива по таймеру</legend>
				<div data-role="fieldcontain">
					<label for="s_16463">(16463) Активация:</label>
					<input type="checkbox" name="s_16463" onclick="writeCheckbox(this);" id="s_16463">
				</div>
			</fieldset>
<script>
var checkboxRegisters = {c16463: false};
var elem = document.querySelector("#s_16463");
var loop = setTimeout (function tick() {
   checkboxRegisters['c16463'] = !checkboxRegisters['c16463'];
   checkboxRegisters['c16463'] ? elem.setAttribute("checked", "checked") : elem.removeAttribute("checked");
    loop = setTimeout(tick, 2000);
}, 2000);
</script>