It is 100% correct (and I was saying you CAN run two amps at the same time as you requested), as is the manual. Please check the different routing options (you can follow the yellow lines to see where the signal is going) to make sure you are choosing a routing option that routes the signal through both amp sections.
For example, routing option 7 will send the same signal through both amps at the same time. I just created and saved a preset with two different amps ine AMP A and AMP B sections, and when I come back and load that preset the routing choice remains and the signal is routed as indicated by the routing selection.
(also note the order in which you do it doesn't affect anything either - I tested by choosing AMP A and AMP B before switching to a dual amp routing setup and nothing reverted or changed whilst choosing different routing options)
If you are seeing odd behavior of signal routing changes when you reload your preset, I suggest you open a ticket with IK Support at
http://www.ikmultimedia.com/contact-support/mi/ and they can see what is going on and resolve your issue directly.
Edit - and yes, I admit that routing changing on its own like that is super odd which is why IK Support would be best suited to help. Very strange behavior indeed, never have seen that!