Hi Cedric,
Are you using KSDK_1.3 with your PE enabled project?
Can you post your project or a simplified version of it?
I've attached example project test_frdm-kl03z_tpm_pwm_pta6_pe_gpio.zip (KDS_3.0+KSDK_1.3+PE for FRDM-KL03Z) that auto configures GPIO and then code toggles it.
Regards,
David