Issue with Batch processing and Actions

I see no reason to flatten the document to destroy one's work.  However, to Automate all I had to add a little scripting the the action. I can not record tool useage Adobey Disables that feature on me,

ConvertBackground.jsx

// A Photoshop Script by JJMack's used by Photo Corners Action
// This script targets the bottom layer and makes sure it a normal layer.
// This script is supplied as is. It is provided as freeware. 
// The author accepts no liability for any problems arising from its use.
/*
<javascriptresource>
<about>$$$/JavaScripts/ConvertBackground/About=JJMack's ConvertBackground.^r^rCopyright 2009 Mouseprints.^r^rScript utility for action.^rNOTE:Convert Background to normal layer if there is one!</about>
<category>JJMack's Action Utility</category>
</javascriptresource>
*/
// enable double-clicking from Mac Finder or Windows Explorer
#target photoshop // this command only works in Photoshop CS2 and higher
// bring application forward for double-click events
app.bringToFront();
// ensure at least one document open
if (!documents.length) {
   alert('There are no documents open.', 'No Document');
}
// if at least one document exists, then proceed
else {
   main();
}
///////////////////////////////////////////////////////////////////////////////
// main - main function
///////////////////////////////////////////////////////////////////////////////
function main() {
try {
// declare local variables
var layers = activeDocument.layers;
activeDocument.activeLayer = layers[layers.length-1]; // Target Bottom Layer
activeDocument.activeLayer.isBackgroundLayer=0; // Make it a normal Layer
}
// display error message if something goes wrong
catch(e) { alert(e + ': on line ' + e.line, 'Script Error', true); }
}

SetSamplerColor

var orig_ruler_units = app.preferences.rulerUnits;  
app.preferences.rulerUnits = Units.PIXELS; // Set the ruler units to PIXELS  
for (var s=0,len=app.activeDocument.colorSamplers.length;s<len;s++) {  
var colorSamplerRef = app.activeDocument.colorSamplers;  
app.foregroundColor=colorSamplerRef.color;
}   
app.preferences.rulerUnits = orig_ruler_units; // Reset units to original settings