I'm going out on a limb here, but having owned several Fullfields and I currently have a couple of Short Mags, they are supposedly almost 95% light transmission with the coatings that Burris uses. I have NEVER had a problem with it being too dark to pick out a deer during any legal shooting hours here in KY, which is 1/2 hour before dawn to 1/2 hour after dusk. You say that most of your shots are 50-150 yds, which shouldn't be a problem for any decent quality scope at all. I'm not saying anything, but I think that it was probably too dark to be shooting at a deer, in general.
When it gets dark, you need to crank up the magnification to 6x or so, higher power helps with the twilight factor of any scope by making things more defined. It reduces the exit pupil, but increases definition. Does your scope have the Ballistic Plex in it? I've found that once it's in that 1/2 after dusk period, the plex tends to fade out since it's so fine, and that a regular Duplex type is much better.
The ultimate low light scope is an 8x56 fixed power, as it has the largest exit pupil that the human eye can take advantage of (which is 7) and a huge objective to gather as much light as possible. It's popular in Europe for night hunting of boars. Many of them have very thick heavy Duplex reticles or post reticles.
I don't think that going over a 40mm lense is going to help you, honestly. I'd stick with the Zeiss if you like it, but get the 3-9x40. I think that it's better than the Leupold in clarity and definition, which will help you more than light transmission will. If you're losing the X-hair, get a heavy duplex type or one of the post types, with a clearly defined aiming point that shows up against the darkest possible background. If most of your shots are less than 150 yds, the ballistic plex (if you've got it) of the Burris is more of a hinderance when the light is dim, and you're not really taking advantage of the long range aiming points anyway.