Sounds like you are using Applications to do the booklets.
Try and not do that , that way all booklets will be done the same no matter the application.
So when you click File > Print make sure the application is not messing with anything. So in Acrobat do not go into Booklet, just leave it as Actual Size (If Letter LEF) or Fit (If smaller than Letter LEF)
Now go into the printers settings via the Printer button, then straight into Fiery Features > Full Properties > Layout > Booklet > 11*17 and it is suggested to set the covers to Print on Both Sides as EFI tends to always assume a cover, even when not defined. So page 2 would always be blank by default, make sure Shrink to Fit is not enabled.
Then go to the Finishing tab and set it to Output tray = Booklet output tray, Fold = Booklet Fold, Staple = Center
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This will print a proper booklet from any application as long as the original document is Letter LEF.
In a preimposed booklet you skip the Booklet layout all together, set it to Tabloid paper in the media tab and make it Duplex Top-Bottom
I won't get into Indesign, too many variables.
Think of it this way, all the programs have those little features to support printers that do not have them.
Even Microsoft says to print with Acrobat/Reader when printing to a production machine, it is built on Postscript and is the standard in print. Adobe does too. But I would suggest PDF/x3, as it is by far the most supported from all the printer manufacturers and RIPs.