AVCHD thru Premiere CS4 encodes hiccups in audio

I need some help with a problem that I can’t seem to find any information about.
First the project - I have a player that I have developed in Flash that reads an audio-only FLV file and uses the FLV’s embedded cue points to load “slide images” as they are needed. The initial video has been shot with a Canon HF20. I am editing the files directly from the camera and from an external eSATA drive with Premiere Pro CS4. In Premiere, I am combining the MTS files and adding the cue points using the video to reference when the presenter changes the slides. The audio sounds perfect in Premiere. I then export the audio as an FLV (I have also tried using F4V to try and fix my problem).
Now the problem – The audio files, which vary in length from 2 minutes to 2 and a half hours, come out of the Adobe Media Encoder with spots of skipped audio (as if they had been dropped frames when encoding). A couple of times I’ve even had “misplaced” audio – where a second or two of audio from one part of the file plays in another section. Listening to the same file more than once shows the problem is in the file, not a playback error (such as something else being processed in the background causing the skip). Also, AME does not report any compiling errors for these files.
Here’s the technical stuff -
Original files are AVCHD from the Canon HF20. Premiere gives the files’ frame rate as 29.97 and audio format as 48000 Hz, compressed, Stereo and the project’s audio format as 48000 Hz, 32 bit floating point, Stereo.
I am encoding the files as audio only, bitrate 96kbps, Stereo for the FLVs and 44.1kHz, bitrate 96kbps, Stereo, using AAC for the F4Vs.
My computer’s specs are Pentium 4, 2.8 Ghz with 4 GB of RAM. XPPro with SP3. I am encoding the final FLV’s to an external 1 TB HD connected via eSATA.
I appreciate any help/advice that anyone might have on this. I know my computer isn’t the best for video editing, but the main reason for this setup was to process the camera’s digital files to audio. If the computer’s processor is what’s causing the hiccups, then I’ll need to upgrade. If you need any more info from me, please let me know. Thanks again!

Hello.
My  system: 8 gb & Win7 x64 & Q9650.
Upgrade to i7 or upgrade to 16 GB ???
I think to wait CS5. Then ...
Many thanks.

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