Thanks for your replies. I guess I just need to scrape more of the winter rust off (mag trainers are not like the real world), and realize I won't get a speed increase of any great magnitude. The FX will still be more efficient for any long rides I may do this year, and climbing with it is so much better.
No I'm not comparing end of season to start of season, I'm comparing results this week.
The gearing is different between the bikes, the Navigator is 14-34 on the rear, and the FX is 11-26.
I did a roll out calibration of the inverts on the Navigator, because the programmed tire sizes didn't match. The programmed 700x32 seems to match the tires on the FX (compared to distance results from the Navigator).
As for any changes to make my hybrid more "road" like - I chose to forgo those when I made my decision between the FX, and The Pilot series. I just didn't want a road bike (I don't like the hoods, and I'll never use the drops). If I have to give up some speed, I guess I'll live with it. The FX already has 700x32 110psi Race Lite Hardcase tires, maybe when they wear out I'll try 28's - I'm still getting use to the handling on the 32's.
Rob