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You could try converting the files to use the same audio type using a package like VirtualDub. It allows you to encode the sound steam of an Avi using any codec and sample frequency you choose (assuming you have the necessary codecs installed).
In addition Vitualdub will probably also allow you to join the files directly. It can re-encode the sound, without touching the video. I think you need to choose "Full Processing" for the audio, and "Direct Stream" for the video.
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