I investigated this with a client and the problem seems to be from the actual clock configuration/crystal oscillator. Unfortunately, we can't reproduce this on our boards, all of them are working well.
Please try another S32SDK example, a PIT or an example which is using the external clock as well, because the gpio sdk example is using the internal clock.
I have tried the example of Hello_World_PLL_Interrupt_MPC5744P from S32DS, this example can execute correctlly in MPC5744P.
however, the example from simulink can not execute in my board.
Thank you for testing that! Unfortunately, we did not solved this issue yet, but please tell me all the marks from the micro controller. For me is SPC5744PFMLQ9 1N15P QMZDR1913A mounted on the SCH-29333 REV E1 - 700-29333 REV A.
Please send me yours and I will ask this further.
Hope this helps,