After you installed the new bios did you do a reset back to factory defaults either via the jumper / switch or in the bios by loading defaults on the first menu?
It sounds like your cd rom drive is an IDE drive and maybe the IDE controller (JMicron controller) is turned off in the bios. Do a reset to defaults and then check and see if the IDE controller is turned on and it should be found by windows then. If not you've got something strange going on...
Also just so you know in the future, you can use a USB flash drive to boot from and do the bios updates. That's how I do mine and it's alot easier to deal with then a floppy. I use an old 512mb drive for it, not good for too much else. Take a look in Ace-a-rue's signature for a link on how to update the bios, and at the bottom of his post is instructions on where to get the HP format utility and such.



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