[Yo-Yo]

Take it in to your Toyota dealer. I have no personal knowledge of the Scion FR-S, but a bit of googling turned up an known issue with them. It seems that the gas tank is really split into two subtanks with an interconnecting pipe.

It's possible that crud has partially blocked this pipe, so that you're no longer fully filling both tanks.

Here is a forum link explaining another guy's problem:

http://www.ft86club.com/forums/showthread.php?t=74249

And here is his hand-drawn schematic of the fuel tanks:

[robroys woman]

Looks like you nailed it. Thanks!