Solved
Program not properly resetting FreeRTOS tasks.
I started off taking Method 3 from https://touchgfx.zendesk.com/hc/en-us/articles/205074561-Connecting-the-UI-to-your-system and it ran fine even after reset or power cycle. I added two FreeRTOS tasks to handle SPI2 and timer2. I flash the target board from inside TouchGFX by pressing Run Target. The board flashes fine and my program works as intended. However, when I reset the board or power cycle the device, my SPI and timer tasks do not run. However, the rest of the application runs fine. Any idea on what could be causing reset to break the program? I want to be able to reset or power cycle and still run my program.
