As far as I know, she become disenchanted, like some others, with the direction Pakistan was heading towards. After Jinnah's death, the situation in Pakistan continued to worsen and Liaqat Ali Khan played a key role in this. He started Islamisation of Pakistan with his vague objectives resolution, he didn't stop the violence against Bengali and Sindhi Hindus who were not planning on leaving Pakistan and he sidelined all those who didn't agree with his vision for Pakistan. This included Fatima Jinnah who dropped out of the spotlight and her last public tour was to East Pakistan in 1954.
There is an article on Times from 1964 about Fatima Jinnah and it discusses her disenchantment with the country. Unfortunately, Times now requires a subscription so you can't read all of it. Here is a link to it:
Pakistan: Trouble with Mother
There are a few more if you search her name on Times, and they all mention what she had been up to before her resurgence.
Due to our doctored history, Liaqat Ali Khan is portrayed as Jinnah's right hand man, but this might not be the reality. Here is a summary of their relation and Fatima's involvement.
While Liaquat Ali Khan is generally regarded as Jinnah's right hand man, this may not be entirely true. Dr Hamida Khuhro's biography of her father reveals that Jinnah told Mr Khuhro "
The prime minister (Liaquat) is average while the remaining cabinet is below average". They are believed to have differning opinions on the issue of minorities. When Mr Jinnah was convalescing in Ziarat, only 2-3 weeks from his death, Liaquat Ali Khan and Chaudhry Muhammed Ali arrived unannounced one evening. "
Do you know why they have come" Jinnah asked his sister and dismissing one of her theories replied "
They have come to see whether I will live or die". Shortly after the visit Mr Jinnah told his physician that it did not matter whether he lived or died. When Mr Jinnah arrived in Karachi on the last day of his life (11 September 1948), an ambulance sent to him wihout fuel, which hastened his end. The Prime Minister had been adivsed by the Military Secretary of the Governor General not to come to the aerodrome. Indeed the Prime Minister reached the Governor General's house after his soul had departed his frail body. Two pages from Miss Fatima Jinnah's book 'My Brother' were censored out while his physician's book was proscribed in 1948 only to be released in 1976 on Mr Jinah's birth centenary. Here the two are seen easing their tension through nicotine.