Buskopan,
забудьте о document.all
<!DOCTYPE HTML>
<html>
<head>
<title>Untitled</title>
<meta charset="utf-8">
<script>
function BunkChange() {
var b = document.getElementById('transport'), c = document.getElementById('shore');
if (b.value =='HELI') {c.value = 'Zabrat'} ;
if (b.value =='BOAT') {c.value = 'SeaPort'} ;
}
</script>
</head>
<body>
<form name="addcrewchange" method="post" action="tba" id="MyForm">
<div class="NavSectionHeader">Please Provide With Details</div>
<table>
<select name="Transport" id="transport" class="FormFieldMed" onchange="BunkChange();">
<option value=""></option>
<option value="HELI">HELI</option>
<option value="BOAT">BOAT</option>
<option value="OTHER">Other</option>
</select>
<select name="shore" id="shore" >
<option value=""></option>
<option value="Zabrat">Zabrat</option>
<option value="SeaPort">Sea Port</option>
<option value="Other">Other</option>
</select>
</table>
</form>
</body>
</html>