I set the ALthold on my quad.
It works fine with a 4S LiOn pack but when i connect MyLiPo 3S 850mah, the quad jumps and keep climbing.
The hover throttle is, more or less, the same.

Why will the power source affect AltHold? Do you have a barometer onboard or externally connected to the FC?

If the hover throttle value is the same then the resulting lift on a 3S should be less than a 4s lion. 

Unless your 4s lion pack was struggling to provide the required amps and you adjusted the throttle value according to that deficiency and now on a lipo pack the system is able to draw more amps to meet the expected throttle value.

Hi, thanks for reply.
The FC is an Omnibus nano v6.2, the onboard baro is the BMP280.

The Lion pack is a 4x samsung 18650, homemade and well working. 3000 Mah, its weight is 206 grams
The Lipo battery is an Infinity 3S, 850 mah brand new, 85C, weight about 70 grams.

I use a spring-centered throttle, i set the curve so i can hover with few inputs, tthe battery compensation is ON. This throttle curve works well with both batteries.

Concerning the configurator, the hover trottle is set on 1430