I believe the earlier throttle bodies (I think Gen 1?) the secondaries should not be moved by hand (risk of getting them out of sync and or damaging the motor), these TB's had a big nut like thing on the front you could turn to open them.
The Gen 3's I can confirm you should be able to freely move by hand, and the bike will cycle them at ignition on so they can find their position. Gen 2 I can't be sure, but looking at the parts online they look similar to the Gen 2.
Does it sound like they actuate when you turn the bike on? If you plug everything in to the airbox / sensors, I believe not having the fuel tank connected won't throw a code, so you can see if the bike actually moves them itself.