The problem with arcade roms is, that some games are identical across multiple systems.
Let’s take a look at 1945kiii.zip
The rom for FBNeo, MAME current and MAME 2003-plus are the same (i use only those 3).
Same name of the zip file, same checksum, same rom files inside with the same checksums:
crc32 FBNeo\ -\ Arcade\ Games/1945kiii.zip
0b7a7ea5
crc32 MAME/1945kiii.zip
0b7a7ea5
crc32 MAME\ 2003-Plus/1945kiii.zip
0b7a7ea5
I will paste only 1 time the content, but it is the same for all 3 zip files
TORRENTZIPPED-B23728B0
Length Method Size Cmpr Date Time CRC-32 Name
-------- ------ ------- ---- ---------- ----- -------- ----
2097152 Defl:X 520095 75% 12-24-1996 23:32 0b9a6474 m16m-1.u62
2097152 Defl:X 521416 75% 12-24-1996 23:32 368a8c2e m16m-2.u63
2097152 Defl:X 664376 68% 12-24-1996 23:32 32fc80dd m16m-3.u61
524288 Defl:X 181385 65% 12-24-1996 23:32 6b345f27 prg-1.u51
524288 Defl:X 84332 84% 12-24-1996 23:32 ce09b98c prg-2.u52
524288 Defl:X 433755 17% 12-24-1996 23:32 bbb7f0ff snd-1.su7
524288 Defl:X 339983 35% 12-24-1996 23:32 47e3952e snd-2.su4
-------- ------- --- -------
8388608 2745342 67% 7 files
The RetroArch scanner is checking your file with the RA databases and 1945kiii.zip
is listed in all 3 databases (FBNeo, MAME, MAME 2003-plus and probably in other mame databases as well)
So RetroArch picks the first that matches.
For this reason you have to use the manual scan method and providing the database that you want to be checked.