Are you talking about the waveform being off-center? I used to get that in my waveforms in Sound Forge, but it would happen when I would use the analog line-in on my computer soundcard to do the transfer (yeah, it sucked...) The way I would fix it, in the past, was to run a DC Offset on it.
Initially, if this is the problem, you won't hear it. But, it will lead to nastiness when you start to build on it (like normalizing, eq'ing...) - Its like building your house on a bad foundation.
Hope this helps, but I am not sure if it will.