Ghost in my machine

[357mag]

This might get long so bear with me. I recently had a new motherboard and processor installed at my local shop. Since then I've successfully reformatted my hard drive and reinstalled Win 2000 once. Last night I wanted to do it again and then clone my computer to my Iomega HD drive. When I got to the end of the Win 2000 setup program and the part where it asks you to restart your computer upon restarting it gave me this:

Invalid System Disk
Remove the disk and then press any key

I pressed the space bar and was able to continue. When I started loading my programs every time I had to restart my computer I got the same message:

Invalid System Disk
Remove the disk and then press any key

Again I just pressed the space bar and was able to continue. I brought my computer into the local shop and Roger the tech said it was because I had a zip disk in my zip drive and the computer was trying to boot of that, so I think he went into the bios and set it up so my computer boots from the hard drive first and the DVD drive second and not at all from the zip drive. I brought my computer home and installed a program but upon restarting I got the same message(and I made sure there was no zip disk inserted):

Invalid System Disk
Remove the disk and then press any key

So I brought it back to the shop and Roger again went into the bios and this time set it up so my computer only boots from the hard drive. But I don't want it set up that way cuz when the time comes(and it comes soon for me)
that I want to reformat and reinstall Win 2000 then I won't be able to cuz my computer won't boot from the CD-ROM? So I changed it back, so my computer is currently set up in the bios to boot from the hard drive first and then the DVD drive second, and I think not at all from the zip drive. But I should not be getting this message at all. Why am I getting this dumb message in the first place? Is it because I first used Partition Magic to format my C drive thereby erasing it before running the Win 2000 setup program? Should I dispense with that step and just put the Win 2000 CD in my drive and click install? I posted this same question on PCmag.com and one guy gave me kind of a confusing answer asking me to download a boot floppy with some extra things on it and then he outlined a way to proceed which I printed out but seems to me to be convoluted. So how do I get rid of this message?