This might not be related but I have a noname 40x CD drive hooked up to my 1200 via a 4xEIDE interface. I've hooked up the CD drive with it's own power supply seperate from everything else.
What I've found is that the CD drive has to be switched on before the Amiga or I would suffer similar problems to those you've described above. (Booting 1 time in 20 in particular).
The same thing when I hooked up a Zip Drive instead.
I don't know how these work but maybe your faster CD drive takes a while to get enough power to spin up or something, and it confuses the interface.
