I have a MacBook Pro i7 (late 2011) 15" 2.26Ghz with 8GB and 250 Samsung SSD (540/520), plus a second 500GB drive where CD-ROM Lived) running Maverick 10.9. Runs great. 
Purchased a 1TB HGST (Hitachi) Advanced Drive Format 7200RPM "7K1000 model" 2.5" drive as a second drive (to replace the 500GB).
On first boot, it took 8 mins to finally boot into OSX.
I went to Disk Utility and the new 1TB drive didn't show up, so restarted, and repeated the same action. Still no 1TB drive in Disc Utility or on desktop.
I read these forums, and did my share of searching the web and others had had success (with 2Tb & 4Tb ADF drives) by booting into OSX Install menu and running Disc Utility from their. Thus booted into OSX (from a boot able USB as I didn't have a CD drive) to try initialize the drive in disc utility. Drive still didn't show up, not even grayed out.
I rebooted (waited the 8 mins again - without the second 1TB drive Mac boots in about 12 seconds) and tried disc utility again, nothing.
The 1TB just doesn't show up. I wondered whether the second drive bay was damaged, so I removed the 1TB and put it into a USB Caddy and then tried formatting it in Disc Utility - SUCCESS!!! Drive initialized no problems.
Believing I had solved the problem, I went about the arduous task of reinstalling the 1TB drive in the second drive bay again.
When the Mac finally booted up (8mins plus again) - no drive showed up on desktop nor disc utility. Eventually an error message appeared on the screen saying something like "drive not readable do you want to initialize/ eject" I clicked initialize. The Mac then tried to initialize the 1TB drive again in Disc Utility. It got all the way to the end and then put up a message saying it couldn't complete the initialize. I tried this several times still not success. I removed the 1TB drive again, reinitialized from USB caddy, ran Disc Verify and Repair no problems reported.
I have now re-installed the 500GB drive backing into the second internal bay and the Mac runs fine and still boots in about 12 seconds.
Funny thing is, the new 1TB drive works fine when connected with a USB caddy, however I purchased it as an internal second drive for data to replace the current 500GB drive and the Mac just doesn't like it.
Any ideas would be greatly appreciated.

Purchased a 1TB HGST (Hitachi) Advanced Drive Format 7200RPM "7K1000 model" 2.5" drive as a second drive (to replace the 500GB).
On first boot, it took 8 mins to finally boot into OSX.
I went to Disk Utility and the new 1TB drive didn't show up, so restarted, and repeated the same action. Still no 1TB drive in Disc Utility or on desktop.
I read these forums, and did my share of searching the web and others had had success (with 2Tb & 4Tb ADF drives) by booting into OSX Install menu and running Disc Utility from their. Thus booted into OSX (from a boot able USB as I didn't have a CD drive) to try initialize the drive in disc utility. Drive still didn't show up, not even grayed out.
I rebooted (waited the 8 mins again - without the second 1TB drive Mac boots in about 12 seconds) and tried disc utility again, nothing.
The 1TB just doesn't show up. I wondered whether the second drive bay was damaged, so I removed the 1TB and put it into a USB Caddy and then tried formatting it in Disc Utility - SUCCESS!!! Drive initialized no problems.
Believing I had solved the problem, I went about the arduous task of reinstalling the 1TB drive in the second drive bay again.
When the Mac finally booted up (8mins plus again) - no drive showed up on desktop nor disc utility. Eventually an error message appeared on the screen saying something like "drive not readable do you want to initialize/ eject" I clicked initialize. The Mac then tried to initialize the 1TB drive again in Disc Utility. It got all the way to the end and then put up a message saying it couldn't complete the initialize. I tried this several times still not success. I removed the 1TB drive again, reinitialized from USB caddy, ran Disc Verify and Repair no problems reported.
I have now re-installed the 500GB drive backing into the second internal bay and the Mac runs fine and still boots in about 12 seconds.
Funny thing is, the new 1TB drive works fine when connected with a USB caddy, however I purchased it as an internal second drive for data to replace the current 500GB drive and the Mac just doesn't like it.
Any ideas would be greatly appreciated.