The DB doesn't retain the "Hidden on MFD" or "Cold at Start" values for groups and units respectively. This means that groups and units spawned with MIST will not retain these options.
Simply add these two lines of codes to their appropriate places in initDBs() function to fix:
mist.DBs.units[coa_name][countryName][category][group_num].hiddenOnMFD = group_data.hiddenOnMFD
units_tbl[unit_num].coldAtStart = unit_data.coldAtStart