The schematic sheet numbers are likely incorrect for your project which can result in the output only generating a PDF of a subset of the schematic sheets. While in your schematic, select Tools > Number Schematic Sheets. In the dialog box that pops up, verify that the values in the SheetNumber and SheetTotal columns are correct. The SheetTotal column should have all the same numbers (i.e. 10 for a 10 sheet project), and the SheetNumber column should have a unique number for each sheet (i.e. 1 through 10 for a 10 sheet project). There are also some buttons on the bottom that will update them automatically if desired, or you can adjust them all manually.