Other Parts Discussed in Thread: TIDA-01226, DLPC3439
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The DLPC3439 (and DLPC3440) chipsets both have a pair of two controllers which write to the DMD in parallel. One controller writes to the Left half of the DMD and one controller writes to the right half.
Can you confirm that you are programming both of the EEPROMs on your system with the correct flash binary image? Each controller has its own EEPROM to connect to and grab binary code from. Are you writing different flash binary images to each EEPROM?