It seems I spoke too soon. It's gone on the Linux side as well. CRAP!!! That tells me its defo a hardware issue....
I built a media streaming PC with plenty of storage. I have a Gigabyte ultradurable MoBo, a 120 gig corsair Neutron SSD that is used only for the OS (Formatted 80 gig for Win7, 40 Gig for Ubuntu. Intel i5 processor, 16 gig RAM, and 2 Toshiba 3 terabyte Hds.
Problem is, that after a day or 2, the second HD disappears from my computer, device manager and from disk management. All drives have been formatted and assigned drive letters (in this case E & F) yet F drive just "goes away". Doesnt do it on the Linux side, just Windows

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