When using Hyperdia for planning travel using the Rail Pass, make sure to un-check the following boxes:
- NOZOMI (SHINKANSEN)
- Private Railways
The Rail Pass web site says that there is an extra charge for "Liner" trains, but I received tickets for the "Marine Liner" when requesting a ticket with a Rail Pass from Takamatsu to Okayama, so I'm a still little confused about that. You might want to un-check the "Liner" box just to play it safe. A handful of other trains may require an extra fare, but they are listed on the Japan Rail Pass site, so you may want to review the "Validity" page on the Japan Rail Pass site first.
When you first go to the Hyperdia web site, you won't see the options unless you click the "SearchDetails" text (not the icon). Thereafter the options will always be visible.