TMS320F28377D: Configures the wrong PWM peripherals after combine APP and boot file

Tool/software:

Hi Expert

Customer feedback the boot (start from 0x80000) and App (start from 0x86000) can run properly individually, but once combine them with C2000 hex utility, the PWM1 configuration code with configurate the PWM2 in real test. 

I recommended they to load the boot and app separately then use Uniflash export function to check whether the exported hex file is align with combined hex file, also use the watch point function to see which assembly instructions modified the PWM2 registers. 

Would like to ask more check points to identify this issue.

Thanks

Joe