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I don't think you can change Premiere's behavior on this one. You could export a window dub and use an external player to make notes with.
If you don't need specific timecodes, but just want the audio transcribed, check out the Speech Transcription feature in CS4 (help docs will show you the way). Depending on how accurate the transcription needs to be, this may work for you (though it's been known to be the source of rather comical transcriptions).
If you need a more traditional log and transcript, you probably have two choices...
1) Set a laptop next to your editing computer, and use that to log while you play back on your editing machine.
2) Burn a BITC DVD (DVD with a burned-in timecode window). Drop a Timecode effect on a clip, tweak its parameters to your liking and set "Timecode Source" to "Media". Save this as an effect preset, and then apply it to all your clips (this is much easier in CS4 now, because you can remove the effect from multiple clips at once, when you're done). Export to DVD following your normal procedures. Use this DVD much like in step one. You could also export to something like Flash or WMV, if you were so inclined; those players will keep going in the background if you want to log on one machine, then.
What about clip notes?