Recording via line-in always below the center line

I've been recording music via a line-in input on my sound card for a while now and had no real issues. However, suddenly all recording I do falls below the center line and I have to center the waveform after recording. Ive checked the connections, bought new wires and still it happens.
Does anyone know:
a) what causes this
b) what issues, if any, are caused when making an "off-center" recording?
Thank you everyone for your time.

Wild_Duck wrote:
The evidence pointed to this being just another example of a machine being designed by an engineer who was red hot on the digital side, but unaware of audio design criteria.
That is more and more turning out to be at the heart of a lot of these problems. At the place I work part-time, more and more people are beating a path to our door with what turn out to be analog problems that have been very poorly understood - or in some rather worrying cases, not understood at all because of this. I had all but given up with electronic engineering (because digital is extremely boring), but I'm getting presented with more and more of these ridiculous problems - and an awful lot of them relate to what happens during the processing of an analog signal before digitising it, because that's pretty much what analog electronics is reduced to these days - I/O. Well certainly commercially, anyway.
Sometimes it's quite good fun when digital engineers come in, and either their eyes glaze over, or more often they are genuinely shocked at what they don't know. And we think that it's all pretty basic stuff!
It had a different DC offset depending on which input was selected and then the offset changed as the gain was increased or decreased.
Hmm......as far as digitising audio in a laptop is concerned, the reference (which sets the DC level you see as a centre line) has to be set at half of the potential voltage swing of the preceding line input stage, and the swing itself has to be scaled to the input of the A-D stage. Capacitors are relatively expensive compared to resistors, so they try to include as few of these as possible in the circuitry, and I think that it's more likely that they would try to manage without them. What this means is that if the power supply to the preamp is isolated from the analog supply to the A-D converter reference, then the chances of drift or an offset in the centre line increase considerably, although in reality this drift is unlikely to be excessive, or that significant - hence the 2% figure I quoted above. If you have several different inputs, then it's hardly surprising that shifts occur - if you end up with, say, and extra mic pre with its own small offset getting magnified by the next stage, then getting to 2% should be quite easy!
No, none of these are precision circuits (or anywhere near to them, in fact) - if you want those, then you have to pay more, and use an external converter.

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