Maria Theresa's chief object in establishing her daughters in foreign courts was to provide a behind-the-scenes influence in favour of Austria. Since Maria Amalia continually refused to use her political influence - far too upfront for Maria Theresa's comfort - for any other object than her own purposes (one can argue whether or not they were intended to benefit Parma, but at any event they were certainly not intended to benefit Austria), it would be a constant nagging thorn in Maria Theresa's side that in this small duchy her daughter continued to ignore any attempts to advise her.
Yes, Maria Theresa wanted her daughters to influence their (adopted) courts although outwardly she scolded her daughters and wrote, in Maria Amalia's case, that her only role was to please her husband. As for Maria Amalia using her political influence, I think it was both ways: both for what she (personally) wanted and what the people wanted. She
knew the power/importance of public opinion and demonstrated that she was willing to court it. Certainly, she also didn't lose her influence on her husband, personal or political-wise. Ferdinand could be annoyed with her (and with her vagaries, who wouldn't?) but it was never a permanent anger, and his ministers certainly knew where she stood (Ferdinand never denied her anything and instructed his ministers to fulfill whatever it was she wanted).
However much her other children may have wished to free themselves from her influence, or however they covertly went against her wishes, it was all done with outward respect and they seemed genuinely to wish to stand well with her. This never seemed to be the case with Maria Amalia once she started to take political power in Parma. Whether or not Maria Amalia had actually given up politics for a country life and travel, she did not submit in any further way to her mother and clearly, any views Maria Theresa may have had concerning Parma's political directions were ignored by Maria Amalia and by Ferdinand. It wouldn't take a particular event for Maria Theresa to continue to feel continually provoked and annoyed with the situation in Parma and her conspicuous lack of influence there. In contrast with the other married daughters, both Maria Carolina and Marie Antoinette were respectful to their mother and Maria Carolina certainly pursued a pro-Austrian political policy, and there was certainly no question of Maria Christina's loyalty to Maria Theresa - so Maria Amalia's postition would continue to stand out from the others.
I get your point...Maria Theresa would've perceived Maria Amalia's disinterest in politics later on as not doing her duty, never mind if the 'irregularities' lessened or were totally banished.
I think there's proof that Maria Amalia showed her respect to her mother but in a very
different way from her sisters, i.e. Maria Carolina and Marie Antoinette. Now, as to how this respect was "lost in translation" or not reported to her for there's no proof that she ever gave up her spies in Parma (unless the only respect that Maria Theresa counted was total obedience to her), I cannot say for now.
I also think that Maria Amalia's refusal or disinterest in doing what MT wanted benefited her (Maria Amalia). Unlike Marie Antoinette or Maria Carolina, she was not perceived as working against her (adopted) people. It's very telling that even though she wasn't as active in politics later on, she kept her people's affections.