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LAUNCHXL-F280039C: Custom bootloader jump to application crashing

Part Number: LAUNCHXL-F280039C

Hey,

I have a custom bootloader that I'm working on that i set-up to jump to the flash address 0x90000. When I load the application through CCS (setting up debug configuration only to store at 0x90000 bank) I am able to successfully jump to the application after a reset and everything works fine. 

But if I take the .hex file (intel hex file format) and write it directly to the flash memory it seems that when I go to perform this same jump the application crashes during the initialization of the application (doesn't reach main) and ends up in ITRAP.

Looking at the memory view where the application is stored (0x90000 - 0x95000) they are identical. Is there some set-up that is performed when loading the application from CCS vs writing the .hex file directly to flash?