Is there any difference between saying "I am not really sure where the noise is from" and "I am really not sure where the noise is from"? are they interchangeable?
There is a difference between the two:
I am not [really sure]
You're anywhere between almost completely sure and quite unsure. Really amplifies sure, and really sure means you's as good as completely, totally sure. The not just says you're not that sure yet, or even that you are not that sure at all. The exact amount of uncertainty depends on many things like context and intonation. I suspect a difference between BrE and AmE as well (cf "quite").
I am really [not sure]
You're not sure at all! Here, really amplifies not sure. While not sure implies you have doubts, really makes that stronger: you have serious doubts.
Another, slightly different example would be:
I am not completely happy.
Meaning you're happy, but not 100%.
On the other hand, if you change the order (and replace "not happy" with the more natural "unhappy"):
I am completely unhappy.
Means that you are almost completely unsatisfied; that is almost the opposite of the first version.