Stratix II GX configuration

Good question! The configurations switch is documented in the reference manual but not detectable in the very detailed layout photo Fig. 2-2. It's a kind of mystery, but as I don't have the board, I can't reveal it. I think however, that even without a consistent documentation, you should be able to find out if the JTAG chain ist actually continued or broken at the HSMC connectors, as suggested by the manual. And you could help Altera support to fix the reference manual.