I would recommend, like most others here, to switch the SSD in to the main bay. The optibay slot does support SATA III, but there have been known issues where an SSD in the optibay had fluctuating speeds in tests, ranging from 5mb/s to the normal 300mb/s. This could be what's causing the long loading speed.
Or, maybe there is just something wrong with your OS. I would honestly just do a fresh install with the SSD in the main bay, and copy over any documents/music/etc onto your HDD.