Audio and Video not matching up after compression

I made a video that is 3:18 minutes long and after about 2 minutes, the audio and video don't match up anymore. I have 2 clips in the video that i conformed to 24p in Cinema Tools and i think that they are causing this problem. I noticed that Audio rate of the clips that i conformed, does not match up to the clips which are not. For example, the audio rate of my 59.94 fps clips is 48.0 KHz, and the audio rate of my 24 fps clips is, 19219 KHz. Is there any solution to this problem? I read a post that said i would need to re-digitize the clips, but i don't know how to do this. Can anyone help me?

I still can't figure out how to solve this problem. I tried to resample the audio, but still, same things happening. If you watch the video, the audio goes off about 2 minutes into it. The audio is correctly matched up with the video when i view it in FCP, but every time i compress it, audio goes off in the exact some spot. Here is a link to the video- http://vimeo.com/21619542
Message was edited by: Gray McClamrock

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    Duration : 51mn 20s
    Overall bit rate mode : Variable
    Overall bit rate : 2 937 Kbps
    Encoded date : UTC 1904-01-01 00:00:00
    Tagged date : UTC 1904-01-01 00:00:00
    Writing application : HandBrake 0.10.1 2015030800
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    Format : AVC
    Format/Info : Advanced Video Codec
    Format profile : [email protected]
    Format settings, CABAC : Yes
    Format settings, ReFrames : 4 frames
    Codec ID : avc1
    Codec ID/Info : Advanced Video Coding
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    Bit rate : 2 606 Kbps
    Width : 720 pixels
    Height : 478 pixels
    Display aspect ratio : 4:3
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    Minimum frame rate : 0.167 fps
    Maximum frame rate : 29.970 fps
    Color space : YUV
    Chroma subsampling : 4:2:0
    Bit depth : 8 bits
    Scan type : Progressive
    Bits/(Pixel*Frame) : 0.314
    Stream size : 957 MiB (89%)
    Writing library : x264 core 142 r2479 dd79a61
    Encoding settings : cabac=1 / ref=3 / deblock=1:0:0 / analyse=0x3:0x113 / me=hex / subme=7 / psy=1 / psy_rd=1.00:0.00 / mixed_ref=1 / me_range=16 / chroma_me=1 / trellis=1 / 8x8dct=1 / cqm=0 / deadzone=21,11 / fast_pskip=1 / chroma_qp_offset=-2 / threads=18 / lookahead_threads=3 / sliced_threads=0 / nr=0 / decimate=1 / interlaced=0 / bluray_compat=0 / constrained_intra=0 / bframes=3 / b_pyramid=2 / b_adapt=1 / b_bias=0 / direct=1 / weightb=1 / open_gop=0 / weightp=2 / keyint=240 / keyint_min=24 / scenecut=40 / intra_refresh=0 / rc_lookahead=40 / rc=crf / mbtree=1 / crf=20.0 / qcomp=0.60 / qpmin=0 / qpmax=69 / qpstep=4 / vbv_maxrate=62500 / vbv_bufsize=78125 / crf_max=0.0 / nal_hrd=none / filler=0 / ip_ratio=1.40 / aq=1:1.00
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    Transfer characteristics : BT.709
    Matrix coefficients : BT.601
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    Format : AAC
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    Codec ID : 40
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    Bit rate mode : Variable
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    Channel(s) : 2 channels
    Channel positions : Front: L R
    Sampling rate : 48.0 KHz
    Compression mode : Lossy
    Stream size : 47.9 MiB (4%)
    Title : Stereo / Stereo
    Language : English
    Encoded date : UTC 1904-01-01 00:00:00
    Tagged date : UTC 1904-01-01 00:00:00
    Audio #2
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    Format : AC-3
    Format/Info : Audio Coding 3
    Mode extension : CM (complete main)
    Format settings, Endianness : Big
    Codec ID : ac-3
    Duration : 51mn 20s
    Bit rate mode : Constant
    Bit rate : 192 Kbps
    Channel(s) : 2 channels
    Channel positions : Front: L R
    Sampling rate : 48.0 KHz
    Bit depth : 16 bits
    Compression mode : Lossy
    Stream size : 70.5 MiB (7%)
    Title : Stereo / Stereo
    Language : English
    Encoded date : UTC 1904-01-01 00:00:00
    Tagged date : UTC 1904-01-01 00:00:00
    Menu
    ID : 4
    Codec ID : text
    Duration : 51mn 20s
    Language : English
    Encoded date : UTC 1904-01-01 00:00:00
    Tagged date : UTC 1904-01-01 00:00:00
    Bit rate mode : CBR
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    00:01:50.877 : Chapter 3
    00:03:59.218 : Chapter 4
    00:13:26.285 : Chapter 5
    00:20:57.685 : Chapter 6
    00:32:58.489 : Chapter 7
    00:39:14.031 : Chapter 8
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