Single coil pickups are susceptible to hum. (Not noticeable to being noticeable depending on where you are playing and what's around you). Your Warren Ellis (looked it up on YouTube) and/or Fender Mustang both have single coils so either way. The amp you are using and/or its setting might be exacerbating the problem but I couldn't say.
Try the in-between pickup position (assuming it has one), try playing in different locations around the house and/or borrow another amp which will give you a clue as to what the problem is.
I love single coils and haven't had a noticeable problem and there's no reason why you should have.
Good luck!
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