Hello @hoeldMech
The reason for the issue you are facing is most likely related to the board's version. If you have the MPC5744P rev E, you have to open the FreeMaster_Config block, and please change the Interface to Serial0 and select the PB2 and PB3 pins.

The ready-to-run examples for the MPC5744P come with the setting for a previous revision of the board, where the serial connection to the OpenSDA was UART1. Unfortunately, this has changed and the settings for both Serial and FreeMaster have to be updated.
Also, make sure that you connect the FreeMaster with the board after the application has been started be executing. When you reset or power up the board, it will enter RappID bootloader ( Which you may have already flashed on the board using the S32DS for PA) and will execute the bootloader for 6-7 seconds while it waits for a new application over CAN or UART. Otherwise, it will load the existing application from Flash.
Hope this helps,
Marius