OK, I narrowed down to three games left, but I can't figured out what's wrong. Am I missing more files? My sets are bad? I need to download more files? Here:

Altered Beast (set 2, MC-8123B 317-0066) [folder: altbeas2 - parent: altbeast - size: 2mb]
missing rom: 317-0066.key [size: 8192] [CRC32: ed85a054] [SHA1: dcc84ec077a8a489f45abfd2bf4a9ba377da28a5]

Altered Beast (set 4, MC-8123B 317-0066) [folder: altbeas4 - parent: altbeast - size: 2mb]
missing rom: 317-0066.key [size: 8192] [CRC32: ed85a054] [SHA1: dcc84ec077a8a489f45abfd2bf4a9ba377da28a5]

Captain America and The Avengers (US Rev 1.4) [folder: captavua - parent: captaven - size: 12mb]
missing rom: hh_00-4.2e [size: 131072] [CRC32: 0e1acc05] [SHA1: 7eb6206efad233f9f4ee51102f9fe6b58f0719ea]
missing rom: hh_01-4.2h [size: 131072] [CRC32: 4ff0351d] [SHA1: 15fc2662ff0d32986c4d4d074b985ad853da34e1]
missing rom: hh_02-4.2k [size: 131072] [CRC32: e84c0665] [SHA1: d846f04315af49abeca00314b3d23e1d8c638dcd]

Shinobi (set 3, System 16B, MC-8123B 317-0054) [folder: shinobi3 - parent: shinobi - size: 1mb]
missing rom: 317-0054.key [size: 8192] [CRC32: 39fd4535] [SHA1: 93bbb139d2d5acc6a1e338d92077e79a5e880b2e]

----------
Missing Sets:             5491 of 6550
Wrong SetName Case:       0 [0 fixed]
Wrong Named Sets:         0 [0 fixed]

Missing Roms:             76411 (649 are 'nodumps') of 93518
Missing Bytes:            40gb of 51gb
Missing BIOS Roms:        0 of 89
Wrong Named Roms:         0 [0 fixed]
Wrong RomName Case:       0 [0 fixed]
Wrong Sized Roms:         0 [0 fixed]
Wrong Date/Time Roms:     0 [0 fixed]
Wrong CRC32s:             0
Wrong MD5s:               <n/a>
Wrong SHA1s:              0

Missing Samples:          <n/a>
Wrong SampleName Case:    <n/a>

Missing CHDs:             <n/a>
Wrong CHD Case:           <n/a>
Wrong Named CHDs:         <n/a>
Wrong CHD_MD5/SHA1s:      <n/a>

Unneeded Files/Folders:   0 [0 fixed]

Number Of Sets:           6550
Number Of BIOS sets:      29
Number Of Parents:        1455
Number Of Clones:         3016
Number Of Others:         2079
Number Of Roms:           93518
Number Of BIOS Roms:      89
Number Of Samples:        2436
Number Of 'nodump' ROMs:  649
Number Of 'baddump' ROMs: 478

--

I:\MAMEroms>dir altbeas*.zip
03/18/2007  01:09 PM           128,436 altbeas2.zip
03/18/2007  01:12 PM           695,748 altbeas4.zip
03/18/2007  01:12 PM           668,682 altbeas5.zip
03/18/2007  07:53 AM           668,488 altbeasj.zip
03/18/2007  08:10 AM           848,905 altbeast.zip
               5 File(s)      3,010,259 bytes

I:\MAMEroms>dir captav*.zip
03/18/2007  02:50 PM         7,449,710 captaven.zip
03/18/2007  03:41 AM           176,817 captavna.zip
03/18/2007  03:41 AM           176,825 captavne.zip
03/18/2007  03:41 AM           177,784 captavnj.zip
03/18/2007  03:41 AM           151,248 captavnu.zip
04/06/2007  05:08 AM            26,825 captavua.zip
03/18/2007  03:41 AM           178,188 captavuu.zip
               7 File(s)      8,337,397 bytes

I:\MAMEroms>dir shinobi*.zip
03/18/2007  02:14 PM           472,579 shinobi.zip
03/18/2007  02:14 PM           117,782 shinobi1.zip
03/18/2007  02:14 PM           284,795 shinobi2.zip
03/18/2007  02:14 PM           265,762 shinobi3.zip
03/18/2007  02:14 PM           254,057 shinobi4.zip
               5 File(s)      1,394,975 bytes


E:\dl\MAME 0.113 to 0.114 update>dir altbeas*.zip captav*.zip shinobi*.zip
04/05/2007  01:18 AM             4,291 altbeas2.zip
04/05/2007  01:18 AM             4,291 altbeas4.zip
04/05/2007  01:24 AM           150,030 captavua.zip
04/05/2007  01:24 AM             6,341 shinobi3.zip
               4 File(s)        164,953 bytes

I already tried getting the original files from v0.113 whole collection (raw) and tried rerunning scanner to fix, but same results.