Just because the noise doesn't show up on your original recording but does appear on your final digital audio file doesn't necessarily mean the noise is a result of a digital artifact. For example, you could pick up a ground hum in the analog realm which would ultimately reveal itself in the digital audio file, but it isn't a digital artifact.
At any rate, what is your full set of gear and how it's connected and configured? Things like:
Analog recordings on what media
Recorded using what machine
Playback machine
What cables connecting playback to...
What soundcard / ADC
Recording with what software
The more details you can provide the easier it will be for us to attempt to help.