Yes, that's exactly what it does. The emphasis is only on the first beat.
The best solution is to create your own click track. You can adjust the velocity to emphasize 1,4,7,etc in PRV.
I like to use wood blocks for hi/lo because it is a pleasant tone that generally doesn't get masked by other percussion.
You can also set the metronome to 3/4 and raise the BPM. This is what I usually do.
I do a lot of 6/8, so I set the metronome to 3/4 and double the BPM.
If you are recording live input (instruments or VSTi's) this works fine, but the measures will obviously be incorrectly shown on your screen.