Running it by itself with irotate works.
Thank you. ^_^
Try it with the rom and bios in the same folder as NAOMI.exe
You can add another sleep to the autohotkey script before the line that launches Makaron.
That will make sure the screen has had enough time to rotate before launching it.
(I don't think this is the issue, but it's something else to try)
sleep, 500
Run, C:\NAOMI\NAOMI.exe ikaruga.dat
You an also comment out all the Gui lines by putting a ";" in front of them.
That way the screen won't be blacked out and you can see what's going on until you get it working.