Aha! I just figured something out. In case anyone else encounters this ...
I was having problems with empty pages not being removed at the end of my document when I changed which conditional tags were visible. I ran through the usual suspects (e.g. checking what page number the next document in the book was set to) but nothing worked. Then I read an Adobe knowledge base article ( http://kb2.adobe.com/cps/314/314928.html) that recommended reapplying the left/right master pages. But when I chose Format > Page Layout > Master Page Layout to do that, I got the puzzling warning "The new column layout in doucment.fm seems to overlap other objects on some body pages. Are you sure you want to do this?" I wasn't sure what that was trying to tell me, since I only have one column and a simple page layout. What was overlapping what? But eventually I got the idea of putting the insertion point outside the text frame (by clicking in the margin) and doing CTRL+A to select all. And lo and behold, there were some empty graphic objects scattered around on various pages. When I deleted them, everything worked again. My empty pages are now deleted as specified in Format > Page Layout > Pagination > Before Saving and Printing. One more small step to world domination through FrameMaker. Hope this helps someone else, Philip.
