I must admit I thought I had read that in the D.U.G., but I just went back and checked and it does say both, and as I have never tried it with two disks attached, I am probably wrong.

The problem of the drives not booting is probably due to:
Two old drives - Primary contains files needed to fully boot
Two new drives - 2.0 only put onto Primary
Boot with New master & old master set to slave - both drives contain the files needed to boot, so everything works.
Boot with new slave set to master and old slave - neither disk has had a SW version applied, so boot fails due to missing files.

Just a guess