the checkboxes are a part of a seperate form from the add to car buttons.
change:
<form name="cupcake1_13_ATC_<?php echo $row_rsCaterLunch["PRODUCTID"]; ?>" method="POST" action="<?php echo $_SERVER["PHP_SELF"]; ?><?php echo (isset($_SERVER["QUERY_STRING"]) && $_SERVER["QUERY_STRING"] != "")?"?".$_SERVER["QUERY_STRING"]:""; ?>">
<input type="hidden" name="cupcake1_13_ID_Add" value="<?php echo $row_rsCaterLunch["PRODUCTID"]; ?>" >
<input type="text" name="cupcake1_13_Quantity_Add" value="1" size="4" >
<input type="submit" class="eC_FormButton" value="Add to Cart" name="cupcake1_13_ATC">
</form>
<form action="<?php echo $_SERVER["PHP_SELF"]; ?><?php echo (isset($_SERVER["QUERY_STRING"]) && $_SERVER["QUERY_STRING"] != "")?"?".$_SERVER["QUERY_STRING"]:""; ?>" method="post" name="cupcake1_11_ATC_<?php echo $row_rsCaterLunch["PRODUCTID"]; ?>" id="cupcake1_11_ATC_<?php echo $row_rsCaterLunch["PRODUCTID"]; ?>2">
<br />
<table width="400" border="0" cellspacing="0" cellpadding="0">
<tr>
<td width="45"><input type="checkbox" name="Sandwiches2[]" value="smoked Turkey" /></td>
<td width="355">Smoked Turkey</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="BLT" /></td>
<td>BLT</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="Tuna Salad" /></td>
<td>Tuna Salad</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="Club" /></td>
<td>Club</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="Brie and Apple" /></td>
<td>Brie and Apple</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="Pesto" /></td>
<td>Pesto</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="Hummus Wrap" /></td>
<td>White Bean Hummus Wrap</td>
</tr>
</table>
</form></td>
</tr>
</table>
to:
<form name="cupcake1_13_ATC_<?php echo $row_rsCaterLunch["PRODUCTID"]; ?>" method="POST" action="<?php echo $_SERVER["PHP_SELF"]; ?><?php echo (isset($_SERVER["QUERY_STRING"]) && $_SERVER["QUERY_STRING"] != "")?"?".$_SERVER["QUERY_STRING"]:""; ?>">
<input type="hidden" name="cupcake1_13_ID_Add" value="<?php echo $row_rsCaterLunch["PRODUCTID"]; ?>" >
<input type="text" name="cupcake1_13_Quantity_Add" value="1" size="4" >
<input type="submit" class="eC_FormButton" value="Add to Cart" name="cupcake1_13_ATC">
<br />
<table width="400" border="0" cellspacing="0" cellpadding="0">
<tr>
<td width="45"><input type="checkbox" name="Sandwiches2[]" value="smoked Turkey" /></td>
<td width="355">Smoked Turkey</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="BLT" /></td>
<td>BLT</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="Tuna Salad" /></td>
<td>Tuna Salad</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="Club" /></td>
<td>Club</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="Brie and Apple" /></td>
<td>Brie and Apple</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="Pesto" /></td>
<td>Pesto</td>
</tr>
<tr>
<td><input type="checkbox" name="Sandwiches2[]" value="Hummus Wrap" /></td>
<td>White Bean Hummus Wrap</td>
</tr>
</table>
</form></td>
</tr>
</table>