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RM44L920: SPI1 & SPI3 Pins as GPIO & removing pull during microcontroller boot/reset

Part Number: RM44L920
Other Parts Discussed in Thread: HALCOGEN

Hello,

I'm using RM44L920 (100 Pin package) microcontroller in one of my projects. I am facing difficulty and I need help in the following things 

1) I am not able to control the state of SPI1_CS[3] (Pin number 39 in microcontroller). The moment I power up the board this pin is always HIGH. (I have tried a lot of things and none of them seem to work. I understand that all the mibspi pins can be used as GPIO. In HALCOGEN, i'm selecting it as GPIO, keeping the initial output value as low, Enabling output direction, disabling open drain and enabling pull down). I need to know how to use SPI1_CS[3] as GPIO ?

2) When i power up the board, my loads are momentarily turning on and then turning off (Turning OFF is expected because in my code i have kept them as OFF and i wont turn them ON unless i receive another digital input). I dont want this "momentary behaviour when powering the board" to happen. Why is this happening ? Is it because of the pin states during bootup or something else ? What can i do to fix this ?

Let me know if any extra details are required.

Thanks,

Badri