on my o4 civic ex i removed the oil cap while engine is running i can see the intake valves moving well 1 is moving how it should that is the one nearest to the timing belt the other valve nearest to cyl. 2 is not really moving at all and if it is it is minimal i reved the engine and nothing changed with that valve is that normal i cant see #2 valves to compare.

 

Since you have an EX model, you'll have VTEC (as long as the engine wasn't swapped). As for the secondary valves, they're only activated when VTEC engages (at 2700 RPM's). That only occurs when the engine is under load. So revving the engine up in a stationary position, will not make the valves open.