Hello @MuhammedAhmet
Most likely the boot process after restart is affected by the linker file. The linker file we provide in our toolbox is designed to work with the RAppID bootloader, but since you are downloading the code using Multilink, we must change the linker file.
1. Please go to Matlab and type the following command
winopen(fullfile(mbd_find_mpc_root, 'mbdtbx_mpc577x\src\linker\gcc'))
2. In the newly opened window, please paste the attached linker file (extract it from archive).

3. Type the following command and please replace the p code attached to the archive.
winopen(fullfile(mbd_find_mpc_root, 'mbdtbx_mpc\mscripts\config'))
4. Open your model, select the MPC5775B mcu, then go to Build Toolchain, uncheck the "Default Target Memory Definitions" and in the dropdown please select the newly added MPC57775B_flash_multi.

Now you can build and flash the code using USB Multilink.
Hope this helps,
Marius