Just recapping my last post.

The baddump/nodump counts from my program are:
baddump 127 (or 96 if merges wern't counted)
nodump 175 (same if merges weren't counted)

ClrMamePro's counts are:
baddump 146
nodump 156

I didn't notice before but the total in each case is 302 :-)

As you suggested I turned on Scanner | Advanced | "Show 'baddump' ROMs & inverted CRCs" and hit the scan button. Examination of the Scan Results revealed the cause of the differences. ClrMamePro is treating 29 nodump's in 5 sets as baddump's. Here are the details:

--- Start fragment of ClrMamePro Scan ---
China Gate (US) [folder: chinagat]
baddump a-12 [size: 65536] [CRC32: 0x3c864299]
baddump a-13 [size: 65536] [CRC32: 0xb745cac4]
baddump a-14 [size: 65536] [CRC32: 0xaef814c8]
baddump a-15 [size: 65536] [CRC32: 0x2f268f37]

Hydra (prototype 5/25/90) [folder: hydrap2 - parent: hydra]
baddump hydr1001.bin [size: 65536] [CRC32: 0x3f757a53]
baddump hydr1002.bin [size: 65536] [CRC32: 0xa1169469]
baddump hydr1003.bin [size: 65536] [CRC32: 0xaa21ec33]
baddump hydr1004.bin [size: 65536] [CRC32: 0xc0a2be66]
baddump hydr1005.bin [size: 65536] [CRC32: 0x80c285b3]
baddump hydr1006.bin [size: 65536] [CRC32: 0xad831c59]
baddump hydr1007.bin [size: 65536] [CRC32: 0xe0688cc0]
baddump hydr1008.bin [size: 65536] [CRC32: 0xe6827f6b]
baddump hydr1009.bin [size: 65536] [CRC32: 0x33624d07]
baddump hydr1010.bin [size: 65536] [CRC32: 0x9de4c689]
baddump hydr1011.bin [size: 65536] [CRC32: 0xd55c6e49]
baddump hydr1012.bin [size: 65536] [CRC32: 0x43af45d0]
baddump hydr1013.bin [size: 65536] [CRC32: 0x2647a82b]
baddump hydr1014.bin [size: 65536] [CRC32: 0x8897d5e9]
baddump hydr1015.bin [size: 65536] [CRC32: 0xcf7f69fd]
baddump hydr1016.bin [size: 65536] [CRC32: 0x61aaf14f]
baddump hydr1037.bin [size: 65536] [CRC32: 0xb974d3d0]
baddump hydr1038.bin [size: 65536] [CRC32: 0xa2eda15b]
baddump hydr1039.bin [size: 65536] [CRC32: 0xeb9eaeb7]

Omega [folder: omega - parent: theend]
baddump 6331-1j.86 [size: 32] [CRC32: 0x24652bc4]

Sai Yu Gou Ma Roku (Japan) [folder: saiyugou - parent: chinagat]
baddump a-12 [size: 65536] [CRC32: 0x3c864299]
baddump a-13 [size: 65536] [CRC32: 0xb745cac4]
baddump a-14 [size: 65536] [CRC32: 0xaef814c8]
baddump a-15 [size: 65536] [CRC32: 0x2f268f37]

T-MEK (prototype) [folder: tmekprot - parent: tmek]
baddump 0078c [size: 524288] [CRC32: 0xff5b979a]
--- End fragment of ClrMamePro Scan ---

--- Start fragment of Listinfo ---
name chinagat
rom ( name a-13 size 65536 region gfx3 flags nodump flags dispose offs 0 )
rom ( name a-12 size 65536 region gfx3 flags nodump flags dispose offs 10000 )
rom ( name a-15 size 65536 region gfx3 flags nodump flags dispose offs 20000 )
rom ( name a-14 size 65536 region gfx3 flags nodump flags dispose offs 30000 )

name hydrap2
rom ( name hydr1001.bin size 65536 region gfx3 flags nodump offs 1 )
rom ( name hydr1002.bin size 65536 region gfx3 flags nodump offs 0 )
rom ( name hydr1003.bin size 65536 region gfx3 flags nodump offs 20001 )
rom ( name hydr1004.bin size 65536 region gfx3 flags nodump offs 20000 )
rom ( name hydr1005.bin size 65536 region gfx3 flags nodump offs 40001 )
rom ( name hydr1006.bin size 65536 region gfx3 flags nodump offs 40000 )
rom ( name hydr1007.bin size 65536 region gfx3 flags nodump offs 60001 )
rom ( name hydr1008.bin size 65536 region gfx3 flags nodump offs 60000 )
rom ( name hydr1009.bin size 65536 region gfx3 flags nodump offs 80001 )
rom ( name hydr1010.bin size 65536 region gfx3 flags nodump offs 80000 )
rom ( name hydr1011.bin size 65536 region gfx3 flags nodump offs a0001 )
rom ( name hydr1012.bin size 65536 region gfx3 flags nodump offs a0000 )
rom ( name hydr1013.bin size 65536 region gfx3 flags nodump offs c0001 )
rom ( name hydr1014.bin size 65536 region gfx3 flags nodump offs c0000 )
rom ( name hydr1015.bin size 65536 region gfx3 flags nodump offs e0001 )
rom ( name hydr1016.bin size 65536 region gfx3 flags nodump offs e0000 )
rom ( name hydr1037.bin size 65536 region sound1 flags nodump offs 0 )
rom ( name hydr1038.bin size 65536 region sound1 flags nodump offs 10000 )
rom ( name hydr1039.bin size 65536 region sound1 flags nodump offs 20000 )

name omega
rom ( name 6331-1j.86 size 32 region proms flags nodump offs 0 )

name saiyugou
rom ( name a-13 size 65536 region gfx3 flags nodump flags dispose offs 0 )
rom ( name a-12 size 65536 region gfx3 flags nodump flags dispose offs 10000 )
rom ( name a-15 size 65536 region gfx3 flags nodump flags dispose offs 20000 )
rom ( name a-14 size 65536 region gfx3 flags nodump flags dispose offs 30000 )

name tmekprot
rom ( name 0078c size 524288 region user1 flags nodump offs 0 )
--- Start fragment of Listinfo ---

Finally you said that ClrMamePro doesn't count nodump biossets - the scan output indicates differently:

PS Arcade 95 [folder: psarc95]
nodump: coh1002e.bin

Cheers,
Tim