Do you have the same issue on the simulator ? Also can you try see what is invalidated when running the simulator ? (press F2 when the simulator is running)
F429 is not powerful enough to be used efficiently with huge display like 1024x600. I don't know if it could have an impact in your case but it's important to take that into account.
Your display is an LTDC display ? Please provide more information about your current setup (software versions, board, external flash, external ram, etc.)
Did you check your clocks ? What's your display clock speed ? Are your framebuffers in external SRAM ? What's the bandwidth of this SRAM ? Same for Flash.
I suspect your clock frequencies are two low and the bandwidth is limited.