During this morning maintenance, the acl version has been updated to v1r35p17 that enables relative thresholds for the control of rotor frequencies.
After acl update, We first restarted successfully the setup with previous absolute threshold.
Then we moved to relative threshold with following lines

define {ROTOR-REL-PARAM} "1 0.01 0.1 0.5 0.95" in "NEB_NCal.cfg"
ACL_PULSE_CH_OPTION {NCAL}_rotor ncal {ROTOR-REL-PARAM} in "NEB_Ncal_shared.cfg"

With this new setting, all rotors successfully reached their nominal frequencies and phases.