Please answer my questions above.
The problem obviously is that when the screen opens it thinks the AGA chipset is not present and thus depth is limited to 16 colors. Later it knows that AGA is present and no limit applies.
The cause most likely is that the screen is opened before necessary drivers have been run. SetPatch, Devs/Monitors and IPrefs are the necessary programs to run before the screen opens.
Two more questions to answer:
Do you have anything in Devs/Monitors?
Do you have some kind of boot picture installed?
