I agree that:
"Leadwerks Engine" is long.
The engine has to be differentiated from the company.
However, the company must not promote 2 names, especially being focused on a single main product
Reasons to not go with Leadwerks3D:
"3D" seems to refer to rendering only, and not the game engine. Think Ogre3D
Engine has no negative connotation in my humble opinion, but I'm curious to hear people's opinion
The main product branded with Leadwerks is the engine, as as such would really rarely create a confusion with the company itself.
The "Software" suffix is enough to differentiate the company in these cases.
Single-word is simply bad.
Typography geeks would probably disagree that a single-word is better to give balance to capitalization.
Suggestions:
Leadwerks 3 (companies don't have a version number)
L3 as an abbreviation. (Pun on 1337 speek for the previous people who would look for the "Engine" in the name.
Leadwerks 3D, if you really care for that name, please add a space.