Placement of logo action Inconsistent. What gives?

You did not answer my question are all image the same resolution and size  does your logo  have the same resolution as  your image.

4x6 is  2:3 portrait aspect ratio indeed.  However there is a big difference in size between a 4x6 100DPI image and a 4x6 300DPI image. one has 240,000 pixels the other has 2,160,000 pixels. 

It is tricky to handle image size with actions.  My action uses a little utility script I wrote in it process a couple of times.

I have also posted a script to place logo on the bottom right of images.  The script resizes the logo to fit the image's size.

#target photoshop; 

app.bringToFront(); 

var logoFile = "~/Desktop/JJMack.png"; // Watermark file should be large for resize down works better than up

var LogoSize = 10; // percent of document height to resize Watermark to

var LogoMargin = 1;                                         // percent of Document height the Watermark should have as a margin

placeWatermark(logoFile, LogoSize, LogoMargin);             // Place Watermark  into the bottom right of document

function placeWatermark(Image,Size,Margin){ 

  if(!documents.length) return;   // if no document return

  try{ 

  var doc = app.activeDocument; // set Doc object to active document

  app.displayDialogs = DialogModes.NO; // Dialog off

  var strtRulerUnits = app.preferences.rulerUnits; // Save Users ruler units

  var strtTypeUnits = app.preferences.typeUnits; // Save Users Type units

  app.preferences.rulerUnits = Units.PIXELS; // work with pixels

  app.preferences.typeUnits = TypeUnits.PIXELS; // work with pixels

  var fileObj = new File(Image);                 // the passed file

  if(!fileObj.exists){   // If file does not exits tell user

  alert(fileObj.name  + " does not exist!"); 

  return; 

  } 

  placeFile(fileObj); // Place in file the Watermark png file

  activeDocument.activeLayer.resize(100 ,100,AnchorPosition.MIDDLECENTER); // Insure Place did not scale layer 

  var SB = activeDocument.activeLayer.bounds; // get layers bounds

  var layerHeight = SB[3] - SB[1]; // get layers height 

  var resizePercent = (100/layerHeight)*(Size/100*doc.height.value); // Percent to resize by

  activeDocument.activeLayer.resize(resizePercent ,resizePercent,AnchorPosition.MIDDLECENTER);  // Resize width and height by percentage

  SB = activeDocument.activeLayer.bounds; // get resized layers bounds 

  activeDocument.activeLayer.translate(-SB[0].value,-SB[1].value); // Move resized layer to top left canvas corner

  var LayerWidth = (SB[2].value - SB[0].value); 

  var LayerHeight = (SB[3].value - SB[1].value); 

  marginSize = Margin/100*doc.height.value; // move resized watermark into the document lower right corner with some margin

  activeDocument.activeLayer.translate((doc.width.value -marginSize - LayerWidth),( doc.height.value -marginSize - LayerHeight));

  }

  catch(e) { alert(e + ': on line ' + e.line); } // inform user of error 

  finally{ 

  app.preferences.rulerUnits = strtRulerUnits; // Restore user ruler units 

  app.preferences.typeUnits = strtTypeUnits; // Restore user type units   

  }; 

};

function placeFile(placeFile) { 

    var desc21 = new ActionDescriptor(); 

    desc21.putPath( charIDToTypeID('null'), new File(placeFile) ); 

    desc21.putEnumerated( charIDToTypeID('FTcs'), charIDToTypeID('QCSt'), charIDToTypeID('Qcsa') ); 

    var desc22 = new ActionDescriptor(); 

    desc22.putUnitDouble( charIDToTypeID('Hrzn'), charIDToTypeID('#Pxl'), 0.000000 ); 

    desc22.putUnitDouble( charIDToTypeID('Vrtc'), charIDToTypeID('#Pxl'), 0.000000 ); 

    desc21.putObject( charIDToTypeID('Ofst'), charIDToTypeID('Ofst'), desc22 ); 

    executeAction( charIDToTypeID('Plc '), desc21, DialogModes.NO ); 

};