Mpeg audio stutters after import - Premiere cs4.2.1

Hi,
I'm trying to import an MPEG video file into Premiere, but the audio does not come in clean.  The source file plays fine through windows media player & VLC.  I've been able to import other files ok, but the program seems to have problems if the audio uses Intensity Stereo.  Has anyone come across this before?  In the past I was able to import these fine into Premiere Elements - but have now changed to Pro.  The stutter occurs both in playback through premiere and if I do export out the video.
I have tried installing other codecs and even tried to replace the ac3 dll - but that hasn't fixed the problem (nor did I really think that was the issue anyway).
Looking forward to seeing what might be the problem, or if I need to change my project settings.
Linda
Here is the media information of the good & bad file.
BAD FILE:
General
Complete name                            : X:\file2.mpg
Format                                   : MPEG-PS
File size                                : 1.31 GiB
Duration                                 : 47mn 20s
Overall bit rate mode                    : Variable
Overall bit rate                         : 3 954 Kbps
Video
ID                                       : 224 (0xE0)
Format                                   : MPEG Video
Format version                           : Version 2
Format profile                           : Main@Main
Format settings, BVOP                    : Yes
Format settings, Matrix                  : Custom
Format settings, GOP                     : M=3, N=12
Duration                                 : 47mn 20s
Bit rate mode                            : Variable
Bit rate                                 : 3 684 Kbps
Width                                    : 720 pixels
Height                                   : 576 pixels
Display aspect ratio                     : 16:9
Frame rate                               : 25.000 fps
Standard                                 : PAL
Color space                              : YUV
Chroma subsampling                       : 4:2:0
Bit depth                                : 8 bits
Scan type                                : Interlaced
Scan order                               : Top Field First
Compression mode                         : Lossy
Bits/(Pixel*Frame)                       : 0.355
Stream size                              : 1.22 GiB (93%)
Audio
ID                                       : 192 (0xC0)
Format                                   : MPEG Audio
Format version                           : Version 1
Format profile                           : Layer 2
Mode                                     : Joint stereo
Mode extension                           : Intensity Stereo + MS Stereo
Duration                                 : 47mn 19s
Bit rate mode                            : Constant
Bit rate                                 : 192 Kbps
Channel(s)                               : 2 channels
Sampling rate                            : 48.0 KHz
Compression mode                         : Lossy
Delay relative to video                  : 8ms
Stream size                              : 65.0 MiB (5%)
GOOD FILE:
General
Complete name                            : X:\file1.mpg
Format                                   : MPEG-PS
File size                                : 1.91 GiB
Duration                                 : 1h 6mn
Overall bit rate mode                    : Variable
Overall bit rate                         : 4 122 Kbps
Video
ID                                       : 224 (0xE0)
Format                                   : MPEG Video
Format version                           : Version 2
Format profile                           : Main@Main
Format settings, BVOP                    : Yes
Format settings, Matrix                  : Custom
Format settings, GOP                     : M=3, N=12
Duration                                 : 1h 6mn
Bit rate mode                            : Variable
Bit rate                                 : 3 848 Kbps
Width                                    : 720 pixels
Height                                   : 576 pixels
Display aspect ratio                     : 16:9
Frame rate                               : 25.000 fps
Standard                                 : PAL
Color space                              : YUV
Chroma subsampling                       : 4:2:0
Bit depth                                : 8 bits
Scan type                                : Interlaced
Scan order                               : Top Field First
Compression mode                         : Lossy
Bits/(Pixel*Frame)                       : 0.371
Stream size                              : 1.79 GiB (93%)
Audio
ID                                       : 192 (0xC0)
Format                                   : MPEG Audio
Format version                           : Version 1
Format profile                           : Layer 2
Mode                                     : Joint stereo
Mode extension                           : MS Stereo
Duration                                 : 1h 6mn
Bit rate mode                            : Constant
Bit rate                                 : 192 Kbps
Channel(s)                               : 2 channels
Sampling rate                            : 48.0 KHz
Compression mode                         : Lossy
Delay relative to video                  : 8ms
Stream size                              : 91.3 MiB (5%)

When one Imports Audio (whether Audio-only, or muxed with Video), PrPro needs to Conform that source Audio, and will create CFA (the Conformed Audio) and PEK (Waveform Display) files. Then, one is actually editing the CFA, though that part is basically hidden "under the hood." If something gets in the way of the Conforming process, then corruption can occur.
I would go to the Media Cache, and just Delete the CFA and PEK files. This should probably be done in the OS. When you then Open your Project, the Conforming process should start, and you should see a little progress bar. Let this process complete 100%, and I would not even touch the computer, while it's on-going. When complete, test.
This ARTICLE goes into more detail on Conforming Audio.
Good luck,
Hunt

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