Struggle how?  Describe the difference in behavior between upright and inverted, please.

I'd be kind of surprised if Rogiero* Fiorotti made the timer so that it would work differently upright and inverted.  It's physically possible, though (in fact, you have to specifically make the software so it works the same in both attitudes).  He'd have put a menu entry in there that's specific to that, and whatever the effect is, he'd have made it so that the timer is shipped with that feature turned off (if I put such a thing into my timer, it'd be behind a gate that asked "are you sure you want to do this?").

Are you sure it's the timer, and not the trim of the plane?  Have you run the thing at a constant speed in the wind and looked for differences upright and inverted?  If the plane has issues in one attitude but no the other, and you're running constant speed, that's an issue you should trim out of the airplane first, and then turn the speed regulation back on.

* Apologies on what I am sure is a misspelling.

One of my suggested tests to check the sensor position and leveling is to check lap time upright and inverted.  Time ten laps upright and then 10 inverted being careful with start and stop will give you a good idea.  If the sensor is level, it shouldn't be different upright or inverted.  On a reasonably calm day, you should hear the same start and stops of acceleration in consecutive round loops upright then inverted.

I suggest that you put the sensor on a level table and then read the x and y numbers on Jeti for the sensor.  Next carefully level the plane along the wing cord and wing length, and then install the sensor leveled to give the same numbers on the Jeti box in the plane as on a level table.

How are you mounting the sensor, what is your level pad in the plane?