my guess is that when you are hammering on the note, you are getting a tone from both sides of the string... the one you intended from the side of the string between your hand and the bridge... and an unintended additional tone between your hand and the nut.
IF that is the case, it might be that the A strings are too high at the nut, and bringing it down a little (e.g. deeper nut slots) would let that part of the string dampen against frets somewhere between your hand and the nut and stop the ringing.
that's my guess based on what you've described... but you want to be very careful with changing the nut slots b/c if you take 'em too deep, you kind of have to start over. Test by fretting the A string somewhere in the middle and see if you're getting a tone on each side. Also, talk to whoever installed the new nut and ask their opinion. If it seems to be the problem I described, you should be able to ask the same person to adjust it for you.
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