Why when optimizing a PDF file made by FM12 did I get the message: The PDF document contains JavaScripts that can cause problems while opening PDF in earlier versions of Acrobat.

Depending upon how you created the PDF from FM, FM may insert an empty javascript entry called "FrameMaker"  in the PDF. You can see this in Acrobat if you use the JavaScript tools to check the Document JavaScripts. It's benign, as there is nothing there to begin with. Why it does this, only the engineers know. If it really is an issue, then just delete this (using the Document JavaScripts tool) before optimizing.