Hi Luke,
I've noticed the same thing, mainly when the LFO is directed to amp and is any other wave form than triangle, and also when the amp velocity button is engaged (and then only on certain patches). To be honest, I noticed it a few times and then didn't think anything more about it.
But I do understand what it feels like when you notice something and it starts to bug you. I had the same thing recently with some builders who hung a door with the hinges on (what was to me) the wrong side. Every time I open the door it bugs me, and I'm thinking 'why couldn't they have put the hinges on the other side'. But Her Indoors, i.e. the missis, doesn't see it as a problem and it doesn't bug her one bit. She opens the door and doesn't think about it - zero annoyance. And yet it is the same door!
I complained about it to her, and she said to me, 'Why don't you get them back to change the door round?' and I said, 'But why did they hang it the wrong way in the first place?'. She shrugged her shoulders and got on with cooking our kids' dinner.
Now, I don't know if this helps (and excuse me if I'm sermonising), but I learn a lot from Her Indoors, and two things I 'try' to learn are her ability to accept things as they are and her ability to get on with what's important. For me, the door is a case in point.
It still bugs me though!
Best wishes,
Old Timer.