Hi, is it an Asus board?
Because Asus went cheap on bios chips not too long ago. Now we have the fun of Asus bioses getting confused because of stuff like turning off and similar cruel treatment. The fuck up with your transformer might habe caused a short spike, damaging the settings. In my experience, Asus boards with a confused cheap bios can be brought back with: resetting bios, turning off electricity several times and lots and lots of reboots. There is a reason, I throw that garbage out and got gigabyte. About the 'suddenly ide' drive mess: did you turn back the settings? And the symlinks: just WTF? Just install debianutils, do 'make modules_install install' and /boot will always have the correct files, with nice symlinks named vmlinuz and vmlinuz.old etc...
