I suspect you have an intermittent problem either with your amp or your speaker....most likely one of the tweeters themselves because they are mechanical and can certainly fail for a variety of reasons (and after all that is what you just got back).
The fact that you are observing differences when you move things around but that you cannot easily conclude where it is coming from is also indicative of a mechanical, heat related or volume level related intermittent failure.
Suggestion: Eliminate what you can, change amp completely (borrow a friends if necessary) and see if it goes away. Try speakers side by side and compare them fed with a MONO signal at various levels (and after enough time for things to heat up to normal operating temperatures.
I see you already suspect the x-over but do not rule out a driver problem...if it is giving a nasty load to your amp then it could cause clipping or IMD distortion and this could show up in tweeter distortion first.