Alex, ARSPD_AUTOCAL is a separate parameter, you have to enable it manually (default is disabled), and if enabled need to fly in circles for at least 5 minutes, it then it adjusts the ARSPD_OFFSET value by comparing the groundspeed to airspeed over that timeframe to adjust the ARSPD_OFFSET accordingly. In addition, during power up, the pixhawk will always perform a "self calibration", you cannot disable this and its simply trying to "zero out" the airspeed to zero on power up during all the other initialization checks, this is the reason why I always keep the pitot tube covered during power up being you don't want any air moving over the pitot tube when it does this. The only problem I've found with the new MS5525 sensor is that it will consistently calculate both the ARSPD_CAL value and the self calibration ARSPD_OFFSET value too high which results in the aircraft thinking its flying much faster than it actually is, and depending on the aircraft, this can result in a stall when performing an RTL or other Auto flight modes. Jordi has stated earlier in this post that he will pass along my information to the developers to get this corrected. Until then, you should use caution with any auto flight modes with this sensor, I know my fixed wing aircraft extremely well, so I know the warning signs when they are approaching stall speed independent of what the sensor is indicating.
And tube order does not matter if you have the ARSPD_TYPE set to the default (2 I think?), it will figure out the order based on differential pressure as Wicked Shell stated on August 23rd earlier in this post.
This really is a superior sensor as I stated many times in this post, and until they get the calibration issue sorted out, you need to manually adjust the ARSPD_OFFSET parameter to correct it as I described, but please use caution if you do, you need to understand what you're doing otherwise you risk a stall.