(1) I really doubt that anything diskbuilder does could harm the drives.

(2) "Sick Tux" (more stoned than sick..) means that the kernel was unhappy with the drive(s). Meaning they did not respond, or (possibly) the root filesystem was not found (?).

A peek at the serial port output should tell the story.

The ATA (IDE) standards recommend having the MASTER drive (0) on the END of the cable, and the slave, if present, in the middle.

Cheers