Just got a pro last week Jan 26/2016
Is it still 1.3 as spirit or new firmware. Saved file from spirit and losded into Pro for same heli. It said double click on values different software or something. It did load fine. All works well have not flown yet. Tks John

1.3.2 is the latest FW:
http://www.spirit-system.com/#2

after FW upgrade its always good practice to check Servo centers pitch range as well as Stick input directions.
Also check correct stabilization by rotating Heli in all directions (XYZ) Aileron, Elevation and Ruder.
If you use Spirit Governor, also check it's function without blades.

So fare, I never had any issues with new FW.

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Oxy4max SpiritPro + HW // SOXOS 550, SpiritPro, HW120A V4, 920KV // SOXOS 600, SpiritPro, HW160A, Pyro650 // SOXOS Strike7, SpiritPro, HW160A, Pyro750 // Skywing Spirit Aero // FrSky Horus X10S + Taranis X7 /

I guess that the settings file that you have saved was created with version older than 1.3.2, this is reason why the window appeared.
The window was just telling you what you should do and why it happened. Normally it is not problem, you should only verify if everything is OK because of backward compatibility between profiles.

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Spirit System developer