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On closer look at the waveform, the samples seem to be squared off, even when the maximum level doesn't appear to have been reached. Could this be the sound card doing its own clipping? Any solutions?

I can think of one problem, thats dc offset in the convertors of the sound card. That could happen as a card ages, you can see if this happens by recording a simpel signal and seeing whether the wave goes both sides of the 0 line.

Cheers Anton