I've had this problem come up quite a few times where my composed output file does not seem to be reading the trim box of my document correctly. Composing shifts my artwork a quarter inch to the right and down leaving no bleed on the upper left.
The only fix that I have found is to place my PDF in InDesign and output a new PDF and build on this. I have checked and rechecked my boxes a dozen times and still have the same problem. Any help is appreciated.
I tried to upload my files with this post but kept receiving a database error. The only file that worked was my .fpi file. 4x6, 12x18, 4up Duplex BLD.fpi