We get this all the time at Vortex, it sounds like the same issue here and I'm sure my colleagues at Trijicon and Leupold get this too (because our travel specs are pretty much the same).
For pistol applications, the combination of height over bore (ESPECIALLY on saddle mounts) and the really close distances guys are trying to zero at will max or exceed the travel. This is because the bullet has to rise sometimes a inch or more to cross your line of sight, and even if you can zero at this distance sometimes you are at a such an early part of the ballistic arc that your zero may not work very well for other distances. We recommend zeroing at 25 yards keeping in mind that you are still going to be a touch low up close. To zero at 7, 10, or 15 you more than likely need to use a shim or a canted base.
Remember in the world of carbines a conventional zero, point of impact is 1.5-2" low at close ranges due to height over bore. The same concept applies here.