How come those rectangles are not visible when PDF is opened with Adobe Reader or Acrobat (or what ever reader was used with first screenshot)?
I understood original question so that rectangles were invisible with one reader (probably Adobe Reader or Acrobat) and visible with web-browser (OP didn´t mention which plugin was used, but I don´t think it was Adobe Reader or Acrobat based on the difference between those 2 pictures... but I may be wrong... maybe OP can tell us more about the readers/plugins used in those screenshots.)
My guess is still that first screenshot has been taken from Adobe Reader or Acrobat, and second screenshot has been taken from some PDF reader plugin that doesn´t support button icons same way Adobe´s softwares does.