I have an buddha IDE controller in my A4000D and when I tried to connect a HD and a CD-Rom drive to the controler this happend:
HD and CD-Rom on the same channel, no HD :-?
CR-Rom pri channel and HD on sec channel, no HD :-?
HD on pri channel and CR-Rom on sec channel, HD and CD-Rom :-D
The harddisk was master all the time, both the CD-Rom and HD is of newer date.
And again if the ROM3.1 dosn't find a HD it will wait for a very long time.
Try to connect the devices, so the HD is master on Pri-channel og CD-Rom is master on sec-channel, it worked for me :-D