ya i had similar probablems with my dual drive recently.. i had it like so:

drive 0= master
drive 1= slave

worked fine for about a month, then all hell broke loose, it may or may not be a drive calbe problem.. mine looks fine.. but u really cant tell.. so then i broke down went everyone to try and find the right jumper pin.. and i did.. put it in same set up, still nothing.. jsut a puase at the boot screen.. so i went ahead and did a swap-a-roo on the jumper pins.. like so

drive 0=slave
drive 1=master

and for some gosh darn reason it booted right up.. so im waiting on the new drive cables from david.. and ill put it back the way i orginally had it and try that..