Compiler/MSP430FR5994: SPI is generating interrupt 0

Part Number:MSP430FR5994

Tool/software: TI C/C++ Compiler

Hi,

I have a test code in which SPI is working completely fine. While if I am using the same code in my primary application which runs with custom bootloader then SPI is generating interrupt 0. 

I have probed the SPI pins and it is seen that after 5 clock cycles pass away the data is received on the clock. And as I said the same code is working fine in debuggable configuration.

I am attaching the picture taken at the time of probing the pins. 

System clock  is 8 Mhz and the MCU is master and we are using NOR flash W25Q80DVSSI as SPI slave. It supports upto 108Mhz.

Blue is Clock and yellow is MOSI.