While I still can't get this plugin to work, I have modified the configuration file to save the packaging type selected so that it doesn't reset to "FedEx Box" each time you edit the plugin configuration.
In the file fedex_configuration.php I replaced the following (around line 196):
<?php
$options = array("FEDEX_BOX"=>"FedEx Box", "FEDEX_PAK"=>"FedEx Pak", "FEDEX_TUBE"=>"FedEx Tube", "YOUR_PACKAGING"=>"Your Packaging");
$opts = array();
foreach($options as $key=>$value){
$opts[] = @JHTML::_('select.option',$key,$value);
}
echo @JHTML::_('select.genericlist',$opts,"data[shipping][shipping_params][packaging_type]" ,$this->element->shipping_params->packaging_type ); ?>
with this:
<select name="data[shipping][shipping_params][packaging_type]">
<option <?php if($this->element->shipping_params->packaging_type == 'FEDEX_BOX') echo "selected=\"selected\""; ?> value="FEDEX_BOX">FedEx Box</option>
<option <?php if($this->element->shipping_params->packaging_type == 'FEDEX_PAK') echo "selected=\"selected\""; ?> value="FEDEX_PAK">FedEx Pak</option>
<option <?php if($this->element->shipping_params->packaging_type == 'FEDEX_TUBE') echo "selected=\"selected\""; ?> value="FEDEX_TUBE">FedEx Tube</option>
<option <?php if($this->element->shipping_params->packaging_type == 'YOUR_PACKAGING') echo "selected=\"selected\""; ?> value="YOUR_PACKAGING">Your Packaging</option>
</select>
And that seems to work, at least for me. Back up your existing file first, just in case!