BETA (I think) One of them starts off right in the first area (the town), has a higher-res hud, and a glitchy dungeon-basement-flooded area-thing. EXE file is Jazz3.exe with the Unreal Icon dated 11/16/1999. Also worthy of note there was a Documentation folder containing progress notes (which so happen to state the glitchyness of the dungeon). I suppose this document would be legal to distribute if anyone cares to see? This version has more files in the Textures folder.

ALPHA (this is the one I have and it says alpha on the start up screen)The other starts off with Jazz on treadmill like object, a "Welcome to Jazz Jackrabbit 3D" voice and menu music, a more pixilated HUD, and nicely done dungeon-basement area. EXE file is Jazz3d.exe with a JJ3 icon and dated 10/6/2000. It seems this version has all superiority aside the lower-res HUD (which I dont know where it is stored to be able to replace it with the high-res one). This version also has more files in the Maps folder.
EDIT: Oh yes, and the crosshair doesnt seem to change in this one