Are all the intake valves supposed to be in the.

No. The fact that the computer is disconnected doesn't facture into it. Since the valves are opened mechanically by the dual overhead camshafts, once the engine is stopped, which ever valve is open remains open or vice versa.
The computer controls the variable valve timing mechanisms which only affect valve operation when the engine is running and then only at certain rpm's and load considerations.

What repairs/diagnosis are you performing on the vehicle?