Sorry for late response.
As you call the pin AN03, have you disabled the analog functions of the pin? See. FM3_GPIO->ADE register.
FM3_MFT0_FRT->TCSA0 = 0x0060 will stop FRT -> should be 0x0020 I guess.
Probably attached example can be used as reference (password is cypress). It is an interrupt based frequency measurement.
It was written for a different MCU, but the MFT is identical.