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>
