If I understand your question correctly. It boots with the one drive with windows on, but if You put in any of the other drives it doesn't. Is that it?
Some MoBos will try booting from the first SATA channel with a drive and if that drive is empty (no bootloader) it will not look further. Try...
There are SATA adapters
http://www.ebay.com/sch/i.html?_from=R40&_sacat=0&LH_BIN=1&_nkw=m2+ssd&_sop=15
and also SATA to USB it thats really important to you.
Do tell me if You find a good one. I might need one someday.
It's not common but it happens, happened to me recently also. Brand new WD drive. Should be covered by warranty, but I'm still about to find that out.
And yes, I'm also looking for some software to check hard drives more thoroughly.
I used to have an older version of Stellar Phoenix NTFS/FAT recovery. It had a RAW mode that could find files on drives without a valid partition table. But I don't know how their current version performs. Just realised this wasn't as helpful as I thought it would be =/ Good Luck.
I got a hard drive from work 2 weeks ago, for rendering some large files. The hard drive worked fine for ~1TB and started writing increasingly larger chunks of zeros short there after. The files seamed fine but the content was mostly black. Very irritating when doing work with a deadline...