Mac Mini won't book with new hard drives???

I have a late 2009 mac mini server running snow leopard server. I recently purchased 2 new hard drives as the I believe one of the hard drives was failing. I formatted the 2 drives and installed Mavericks OS X server on one.
When I put the 2 drives into the mac mini, the system won't boot. I just get the flashing folder. If I keep the old (snow leopard) drive in the system and connect the mavericks server disk as an external (USB connected) drive, it will boot and runs just fine.
Am I missing something??
Here are somethings additional facts:
When I have the snow leopard server drive in and it boots from that, it doesn't recognize either of the 2 new drives. Wants to either eject or initialize.
I realize that it can read the newer system.
I have to boot with the option key so that I can pick which drive to boot from.
Any thoughts would be helpful. I'm not sure why it works one way and not the other.
Thank you.

Did you set the Partition Map Scheme to GUID Partition Table before Formatting the Drives Mac OS Extended (Journaled)...?
You can check in a couple of places:
Apple > About This Mac > More Info > Hardware > Serial-ATA
Or in Disk Utility by highlighting the Drive and looking at the Drive info

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MacBook Pro won't boot with new hard drive, but a different MacBook Pro will

So here are the details. My friend and I both have 13-inch Mid 2010 MacBook Pro's. Same processor and specs since they were purchased at the same time, but originally had 250 GB hard drives. His hard drive failed and needed a new one. Put a 500 GB Seagate Momentus 5400.6 in his computer, and tried using a flash drive with "Install OS X Mavericks" on it to install Mavericks on his new hard drive. No matter what, it wouldn't install. I finally was able to install OS X 10.9.4 on it by connecting the new hard drive to my computer with a USB hard drive enclosure. I put the hard drive back inside his computer and it wouldn't boot (stuck on the gray screen with apple logo and a spinning wheel). I then attached to the hard drive to his computer externally with the USB enclosure, and then it booted and worked perfectly.
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but my computer boots with: 1) new hard drive connected externally AND internally, and 2) my hard drive internally.
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If anyone has any idea what's causing this and how to make his computer work with the new hard drive internally that would be greatly appreciated.

So after switching the internal SATA cables from each computer, now we have
His computer, with my SATA cable:
1) Worked with every hard drive!
My computer, with his SATA cable:
1) Works with 1 TB Toshiba hard drive
2) Works with 500 GB Seagate hard drive
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So it turns out you were right! Definitely had something to do with the SATA cables. But it's still strange that mine was able to boot with all the hard drives except the one that was originally in his. So it seems like it was some combination of his SATA cable and something else, since when his SATA cable was in his computer only 1 hard drive (my original) worked, and when it was in my computer, 3 hard drives worked. But at least its working, and I'm just gonna keep our SATA cables switched since that seems to work out fine

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4GB Limitation of Windows NT - Partition with the FAT16 system cannot be higher than 4GB - Fdisk cannot be used for creating, but the Disk manager is used (Disk management in Windows 2000)
8GB - Limitation of the BIOS system. For the support of larger capacities you need extended functions of the BIOS system. Limitations valid for the x86 computers and some motherboards with Pentium and Pentium II processors. Some other operating systems must know how to use the extended BIOS functions (Extended Interrupt 13). We can use Windows NT 4.0 as an example where you need an updated disk driver or the Service Pack. (OS - DOS 6.xx and lower, Windows 3.x and lower and some other older OS do not have the support of the Ext. Int13).
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68GB - Possible problem with disks larger than 67GB under Windows 9x... See article WD800
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thetrudz wrote:
A computer friend can install a hard drive just fine for me. However, I do not have the Leopard install disc.
Hi, and welcome to the forums.
That Mac should have come with Leopard. If so, call AppleCare. They'll send you replacement discs for a nominal fee.
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BDAqua wrote:
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I'd get Temprature Monitor & see what temps they're running.
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Back up all data. Don't continue unless you're sure you can restore from a backup, even if you're unable to log in.
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