You will not believe this but THAT is why I joined this forum..I have been trying to get my old 1995 GW2K back up and running win 98 for my 70 yo mom who just wants a basic entry computer and I thought what the heck lets give it a go. I took the thing to a shop...a reputable computer shop in the area...and they wiped the hdd but could not get past the invalid system disk error message. The thought was just junk it but it has a killer voodoo graphics card and all the stuff my mom would love to use so I would like to get it up and running. Today I went to another computer store and bought a used PC and it would not run either, faulty media something or other so back it goes under 30 day warranty...not even a boot up to be had. Thank goodness I happened to buy a new computer a few yrs ago or I would be back in the stone age with my mom, good company, great place to visit, but wouldn't wanna live there!
I now have a wiped hdd that is error free and shows up on the screen as installed, the floppy says it is installed, the cd rom is who knows where but the motherboard seems to work just fine....

There is a floppy head cleaning disk you can buy might be worth a try saved me a few time. There is a picture of one some guys selling you can get them at most electronics stores
floppy disk drive cleaning kit -rescue that dodgy file on eBay Floppy Drives, Drives Storage, Computing (end time 02-Jul-07 21:08:41 BST)

Did you now the windows 98 CD is bootable as long as you can tell the bios to boot from it.

Yeah but I can't get the cd to be recognized. It was there for a minute and then I was told to make my floppy the first bootable drive and when I did the cd rom drive disappeared. Nevertheless, I did try and get it back, no luck even going into ms dos and plugging in drivers. I thought about doing the old take the battery out overnight trick and see what is up. The cd rom still lights up but maybe it is the silent killer of this pc? It will be interesting to see what happens without the battery.
The pc starts up okay, gets to the installation of the hdd and the floppy and there it stays with the invalid disk message whether there is a disk in or not and when there is a disk in any drive even the a, I get Remove disks or other media and press any key to restart
message. So these two messages keep boomeranging at me

Did you check in the bios if it was set to boot from the floppy drive first? It might be set to boot from the har drive first with would give you this message also if it has been formatted.