Illustrator Scripting :: Batching SaveAs In CS6 Will Not Save PDF Compatible

So I'm using a script that I wrote to bring in files that were converted from CorelDraw to EPS (this is the best conversion process to preserve text and drawing assets).  Basically the script takes the art in the EPS, groups it, places a rectangular border around the art and centers them.  We do this so that they come into InDesign correctly sized.  The problem is, it used to be 100% automated, just about, however now the saveas action command will not remember that "Save as PDF Compatible" needs to be set to true.  When I do a saveas command, it's check by default, but when the saveas command is batched, it does NOT do it that way.  When I try to bring batched AIs into InDesign, it's text that says it was not saved as PDF Compatible.  Am I going to have to script a save function to get control of the saveas settings?  I don't understand why PDF compatible is checked by default, yet batching saveas saves as if it unchecked it.