I edited the startup sequence like you recommended and it still stayed at a black screen upon bootup.
I then commented out the acatune line and the Amiga then booted to a CLI prompt.
I then tried to use kick40068.a1200 and it booted great even with my original startup-sequence.
Sure seems to me that I have a corrupt kick39.rom. I will try again with a different rom..
Update: I just ran acatune -status after booting to OS39 with acatune in the sequence using kick40068.a1200 and it says the maprom function is disabled.. that is incorrect, right? UGH!?!?
Update2: I tried another kick39.rom and still no success.. just sits at a black screen when the Amiga boots. Strange thing I noticed is that if I left acatune in with kick40068.a1200 WinUAE booted fine and then when I did acatune -status it said the maprom function was enabled???? Apparently it is detecting a 28MHz ACA with WinUAE.