FIXED!
I reinstalled Starsector, Exerelin, and all of the Factions. Now the Storage and Omni Factory are spawning properly.
One thing I did notice though in my first game since reinstalling (all of the starting parameters maxxed) is that the Storage/Omni didn't spawn in the system that my faction started in. In the first case so far, it spawned in the Exerelin system even though it said my faction started in another system. Could be because I picked "Fully" for the "how populated is the exerelin system" - but in that case I might have misunderstood that parameter. Does selecting Fully for that mean it is populated by YOUR faction? OR does it just mean that system starts with the maximum amount of planets/stations per your starting parameter choices? Otherwise, it could just have been because my faction took over a station in Exerelin just as the Storage/Omni fleet was generated and it picked that station.
Either way, working great - such an awesome mod!
Running great even with all the starting parameters maxxed (24 systems with the highest possible parameters) - on a custom gaming rig running Java7 64 bit and Starsector set to use 512mb to 4g RAM.
Edit: I don't recommend playing with all 24 systems and maxxed parameters... it takes a very long time to load a save!
Back to conquering the universe!