I didn't see it in the manual. When looking at the backplane, you can see blue keys about 1/4 of the way up the connector. Blue keys are for 5V VIO. Yellow keys indicate 3.3V VIO. This is part of the cPCI spec (page 61 of the PICMG 2.0 R3.0 spec, which is what the PXI spec is based on).
Modules follow the same color code for keys. Additionally, there is an option for a "universal" card, which means it will work with either 3.3V VIO or 5V VIO. Universal cards don't have a key.
The blue and yellow keys differ mechanically to prevent crossing modules and backplanes with different requirements. Universal cards, without a key, will fit into either backplane without interference (as it should be). The keying prevents damage to cards.
Most cards are either 5V or universal. Your card is odd in that it requires you to make this setting manually (a poor design choice to save cost).
In summary, the VIO voltage isn't documented well, but very few people need to know it so it hasn't come up. I'll file a corrective action request for the documentation.
