I don't know how to help you, but to me this seems due to some inefficiencies on the audio routes on the Overo COMs, that sometimes became apparent (maybe due to a slightly different component values on the board, in your case).
I have a similar problem, but caused but the OTG port... and I've not found any solution.
I've you tried to use a different combinations of board and module ?
Experiencing what I suspect is a heat related noise issue with some Overo Water and TOBI board combinations.† Been recording audio using ALSA via the line-in on TOBI and what Iíve observed is that when my equipment starts to warm up (itís outside in a plastic sealed box where the external ambient can rise to ~30C) I get some wandering noise between 12 and 16kHz.† Itís a reasonably powerful tone and screws up what Iím doing with the audio somewhat.†
A related issue is also that of USB hard drive noise appearing to get injected in to my audio recordings.† The drive is written to periodically via the EHCI USB port and the movement of the mechanical portions of the drive appears in my audio file as a form of blipping.† This noise is always present when I have a USB hard drive in the equation, but is of less concern to me than the tone between 12 & 16kHz.†
However, since these particular parts were ordered 28th Jan 2010 and 5th Jan 2010 I would have thought that this improvement was already present in my gear.† The Water board revision is R2516, and TOBI is R2549.
When I record from the same TRS connector in to an Edirol recorder I do not observe the noise in my recordings (same environment and recording source), hence my assumption it is being injected before the audio ADC but after the TRS connector.† Confoundingly, I have a set of Overo Water + TOBI that perform flawlessly in the same environment.†
Anyone experienced this at all before? The ability to capture and analyse audio is critical to my application; I need to either work around this issue or get rid of it entirely.†
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