The count is not wrong...it's just how the stats counts work. The rom count does not care about bios/merge but works on the plain defintions. If you miss a set, every file in its definition is counted as missing (as well as each file is counted for the total). There is a slight exception if no dump chds or no dump roms are included. But such files do not exist at all, while the chd belonging to the set is 'real'.
loveber3cn is a set which consists of a chd (mda-c0071) and bios rom (mb_eeprom_exp.ic54s).
Since you don't have the chd, you don't have the set and so the bios rom is counted as missing (and the set is counted as missing, too).
You don't see a message about a missing chd, since the scan tree output hides it when you disabled chds.
You don't see a message about a missing bios rom, since the scan tree output will only list it inside the bios sets themselved.
You migh not see a missing set message if you're using merged sets since then the existance of the parent + biosrom is enough...
You see....Statistic total/missing counts are based on set definitions, not parent/clone/bios relationsships....forget about the numbers...they don't bring you anything....Look at the scan tree output...if it's empty, you're good...but only related to your chosen check options.
Update: However, I will have a 2nd look at it since if biossets are separated and are available it should be counted as available.....but anyway...don't care too much about these numbers...