I wasn't entirely comfortable with my rip so I picked up another (cleaner) copy of Moto Racer 2. The first time around EAC detected the track 6 pregap wrong. I fixed track 6 correctly, but track 5 was left with a bit of pre-gap stuck to the end. With this fixed the dumps match. On the new disc EAC correctly detected all the gaps at 3.00 seconds.

The corrected Track 5 Hash info is:
rom ( name "moto racer 2 (u) (track 05) [slus-00738].bin" size 37443840 crc 05675cbf md5 99c7a3509d8a1867f017fe9937c5adf5 sha1 7f884e1a8e928df4e685244e59ae4dd17de0cf74 )


clrmamepro output for new rip:

rom ( name "moto racer 2 (u) (track 01) [slus-00738].bin" size 123992736 crc 016221f7 md5 f1e394c394f5191bab9e23706fb4d50f sha1 55d5a4d40817e8798925f030993dc65dd908cc1f )
    rom ( name "moto racer 2 (u) (track 02) [slus-00738].bin" size 25335744 crc d4ba192a md5 43030e7c231e7d6d492f286d22d6de26 sha1 63bd5a3cc35631ba9e142bb7f4b651bc4b281104 )
    rom ( name "moto racer 2 (u) (track 03) [slus-00738].bin" size 20295408 crc 3608e377 md5 b1f93870c54c506f95ae226a9f8e674e sha1 7f04135d2f46cc04c8d99580e41bb181f289a085 )
    rom ( name "moto racer 2 (u) (track 04) [slus-00738].bin" size 29759856 crc d56ee1a8 md5 fb78b76f6eb5bac222f099d2ed12ad4c sha1 8527bf50dce699efa1f5b164b6e56517fe243ef1 )
    rom ( name "moto racer 2 (u) (track 05) [slus-00738].bin" size 37443840 crc 05675cbf md5 99c7a3509d8a1867f017fe9937c5adf5 sha1 7f884e1a8e928df4e685244e59ae4dd17de0cf74 )
    rom ( name "moto racer 2 (u) (track 06) [slus-00738].bin" size 28421568 crc e10bb70e md5 d27923791419bca3347fed5d68ada85b sha1 a92b5c230c48336e2472238d2304e25e72b3af10 )
    rom ( name "moto racer 2 (u) (track 07) [slus-00738].bin" size 24554880 crc db24b453 md5 1e09369b226fe5efefbf594fe1926d6d sha1 ffd1f42f9542f306bef21548a58b9a04207195b1 )
    rom ( name "moto racer 2 (u) (track 08) [slus-00738].bin" size 27563088 crc 9a8f1fa1 md5 ff5ba20ed2e86ac72ce4b02ecd97c0e2 sha1 0b092d94d1cabbfeac08c7e70221c4a56b9670e7 )
    rom ( name "moto racer 2 (u) (track 09) [slus-00738].bin" size 31954272 crc e2f5a5a4 md5 077a6433851db63eb2956e2ccb6b4dd0 sha1 9f8a9a97bf9aa544b6164f152d0e8bbc32e6901d )
    rom ( name "moto racer 2 (u) (track 10) [slus-00738].bin" size 27755952 crc 63f00868 md5 00c0913137d806c35b0413bf15b3a299 sha1 3151239d2af1a27c649f6ff109b42da42d097017 )
    rom ( name "moto racer 2 (u) (track 11) [slus-00738].bin" size 30305520 crc 39347f12 md5 0cb43c0cd635da5c1673ec0685c31801 sha1 1f13ec11d9ea56638c96949758472d08d643acfe )
    rom ( name "moto racer 2 (u) (track 12) [slus-00738].bin" size 25582704 crc aaea80c6 md5 1155c8a94390d1850d94dcf49fb32d25 sha1 0077fe17243664eb646c4df437069c3c110c165b )
    rom ( name "moto racer 2 (u) (track 13) [slus-00738].bin" size 37417968 crc fbaebea1 md5 e8a7f12bb589256398d116eaf3b4142c sha1 148f8cf62c5d8e8c2c0606ea914641ac09f51a9e )
    rom ( name new_dump.log size 4974 crc 6590697b md5 1cb4cdb0d5d509a93e751bce22ca8377 sha1 fbe0b10ae0a4055b9da45eb07b7b5bc9414ca358 )

EAC log:

Exact Audio Copy V0.99 prebeta 4 from 23. January 2008

EAC extraction logfile from 15. February 2008, 16:22

Unknown Artist / Unknown Title

Used drive  : HL-DT-STDVDRAM GSA-H62L   Adapter: 1  ID: 2

Read mode               : Secure
Utilize accurate stream : Yes
Defeat audio cache      : No
Make use of C2 pointers : Yes

Read offset correction                      : 669
Overread into Lead-In and Lead-Out          : Yes
Fill up missing offset samples with silence : Yes
Delete leading and trailing silent blocks   : No
Null samples used in CRC calculations       : Yes
Used interface                              : Native Win32 interface for Win NT & 2000
Gap handling                                : Appended to next track

Used output format : Microsoft PCM Converter
Sample format      : 44.100 kHz, 16 Bit, Stereo


TOC of the extracted CD

     Track |   Start  |  Length  | Start sector | End sector
    ---------------------------------------------------------
        1  |  0:00.00 | 11:45.68 |         0    |    52942   
        2  | 11:45.68 |  2:23.47 |     52943    |    63714   
        3  | 14:09.40 |  1:55.04 |     63715    |    72343   
        4  | 16:04.44 |  2:48.53 |     72344    |    84996   
        5  | 18:53.22 |  3:32.20 |     84997    |   100916   
        6  | 22:25.42 |  2:41.09 |    100917    |   113000   
        7  | 25:06.51 |  2:19.15 |    113001    |   123440   
        8  | 27:25.66 |  2:36.19 |    123441    |   135159   
        9  | 30:02.10 |  3:01.11 |    135160    |   148745   
       10  | 33:03.21 |  2:37.26 |    148746    |   160546   
       11  | 35:40.47 |  2:51.60 |    160547    |   173431   
       12  | 38:32.32 |  2:25.02 |    173432    |   184308   
       13  | 40:57.34 |  3:29.09 |    184309    |   199992   


Track  2

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track02.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 100.0 %
     Copy CRC D4BA192A
     Copy OK

Track  3

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track03.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 99.8 %
     Copy CRC 3608E377
     Copy OK

Track  4

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track04.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 100.0 %
     Copy CRC D56EE1A8
     Copy OK

Track  5

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track05.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 99.8 %
     Copy CRC 05675CBF
     Copy OK

Track  6

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track06.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 100.0 %
     Copy CRC E10BB70E
     Copy OK

Track  7

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track07.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 100.0 %
     Copy CRC DB24B453
     Copy OK

Track  8

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track08.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 100.0 %
     Copy CRC 9A8F1FA1
     Copy OK

Track  9

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track09.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 100.0 %
     Copy CRC E2F5A5A4
     Copy OK

Track 10

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track10.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 100.0 %
     Copy CRC 63F00868
     Copy OK

Track 11

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track11.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 99.8 %
     Copy CRC 39347F12
     Copy OK

Track 12

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track12.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 99.8 %
     Copy CRC AAEA80C6
     Copy OK

Track 13

     Filename E:\Documents and Settings\Administrator.JOHN-16AE90FFA2\My Documents\roms\PSX\new_mr2_dump\Track13.bin

     Pre-gap length  0:00:03.00

     Peak level 89.1 %
     Track quality 100.0 %
     Copy CRC FBAEBEA1
     Copy OK

No errors occurred

End of status report