Hi,
It is a very good idea to test your different lenses when using the Zone System. F stops do not always accurately represent the amount of light that actually makes it through the lens. (T stops do that, and why we don't use them for still photography, I do not know.) There can be differences between lenses based on how efficiently they transmit light. One glaring example that I know of first hand, since I actually did the comparison myself, is the Canon 200mm f/1.8 vs. the new 200mm f/2 IS. The 1.8 is 1/3 f stop faster. But because of the difference in optical design between the two – the new one has IS, for one – the older 1.8 is actually 2/3 t stops faster.
And, as you have seen with your own eyes, different lenses can render things quite differently in terms of contrast.
Just make sure your lens is focused at infinity for the grey card test, and make sure that you are not casting a shadow on the card. It also OK to back up a little if you are having trouble keeping your shadows out of the way. You can take a densitometer reading off of a very tiny area, so backing off a bit won't hurt you. As long as you meter only the card itself, it doesn't matter whether or not it fills the frame.