Hi Hesham,
PFE driver for QNX 8.0 is only in Proof of Concept level and might have some problems which are not resolved yet.
The configuration for PFE use in QNX is a little bit tricky, you need to configure HW and clocks in u-boot before starting QNX, as we don't have SerDes implementation in QNX driver.
APP FSM timeouts means, that FSM clocks are not configured correctly.
I recommend to use u-boot BSP 39.0 with DTB and ATF. Inside this u-boot, there is PFE driver which will configure all the settings before booting QNX.
Please follow PFE QNX Integration Manual from Release package
doc/qnx_drv_im/PFE_QNX_DRV_IntegrationManual.pdf
Regards
Milan