Of course without knowing the details it is hard
to guess the answer.  However, a similar thing
happened to me in the past, so I will share
with you.

We had a good system, then put the lid on it.
The structure of the housing was  contributing
a surprising amount to the frequency of
vibration of the active part.  The lid
changed the vibration properties and
we had a lot of trouble.  When we finally
found the problem we could adjust it.

So, maybe sealing the unit changes the
fundamental frequency of the housing
plus resonator.

best regard
mark

/signaturee