I have seen this happen in Grub many times where it (for some strange reasons) changes the (hd 0,0) to (hd 1,0) or another form of it.
I even had a server with hd 2,0 in the menu.lst file which changed itself to hd0,0 after an upgrade! then no boot!
so always make backup copy of your (Working) menu.lst file BEFORE doing any updates/upgrades or recompiling kernel.
2 cents worth from a noob!