Well, if you don’t trust a piece of closed source software that a lot of people are using without complain, you can do the work manually.
Go to this site: http://adb.arcadeitalia.net/lista_mame.php and cross-check your files with the crc32 values from the site and the values in the *.dat file.
It looks like this (dkong.zip as example):
NAME | SIZE | BIOS | STATUS | MERGE | REGION | OFFSET | OPT | CRC | SHA1
---------------------+-----------+----------------------+---------+----------------------+-------------------+------------+-----+----------+-----------------------------------------
c-2j.bpr | 256 | | good | | proms | 100 | no | d6412358 | f9c872da2fe8e800574ae3bf483fb3ccacc92eb3
c-2k.bpr | 256 | | good | | proms | 0 | no | e273ede5 | b50ec9e1837c00c20fb2a4369ec7dd0358321127
c_5at_g.bin | 4096 | | good | | maincpu | 3000 | no | b9005ac0 | 3fe3599f6fa7c496f782053ddf7bacb453d197c4
c_5bt_g.bin | 4096 | | good | | maincpu | 2000 | no | 1c97d324 | c7966261f3a1d3296927e0b6ee1c58039fc53c1f
c_5ct_g.bin | 4096 | | good | | maincpu | 1000 | no | 5ec461ec | acb11a8fbdbb3ab46068385fe465f681e3c824bd
c_5et_g.bin | 4096 | | good | | maincpu | 0 | no | ba70b88b | d76ebecfea1af098d843ee7e578e480cd658ac1a
l_4m_b.bin | 2048 | | good | | gfx2 | 0 | no | 59f8054d | 793dba9bf5a5fe76328acdfb90815c243d2a65f1
l_4n_b.bin | 2048 | | good | | gfx2 | 800 | no | 672e4714 | 92e5d379f4838ac1fa44d448ce7d142dae42102f
l_4r_b.bin | 2048 | | good | | gfx2 | 1000 | no | feaa59ee | ecf95db5a20098804fc8bd59232c66e2e0ed3db4
l_4s_b.bin | 2048 | | good | | gfx2 | 1800 | no | 20f2ef7e | 3bc482a38bf579033f50082748ee95205b0f673d
s_3i_b.bin | 2048 | | good | | soundcpu | 0 | no | 45a4ed06 | 144d24464c1f9f01894eb12f846952290e6e32ef
s_3j_b.bin | 2048 | | good | | soundcpu | 1000 | no | 4743fe92 | 6c82b57637c0212a580591397e6a5a1718f19fd2
v-5e.bpr | 256 | | good | | proms | 200 | no | b869b8f5 | c2bdccbf2654b64ea55cd589fd21323a9178a660
v_3pt.bin | 2048 | | good | | gfx1 | 800 | no | 15e9c5e9 | 976eb1e18c74018193a35aa86cff482ebfc5cc4e
v_5h_b.bin | 2048 | | good | | gfx1 | 0 | no | 12c8c95d | a57ff5a231c45252a63b354137c920a1379b70a3
Or, if you can coding, write a script that does the work for you
(Don’t fear, i scanned the site for you )
Sorry i am making fun of you, that*s mean…
[EDIT] open source but buggy and incomplete:
[EDIT2] found another one: