That is odd. I have not tested this with El Capitan as I am using Yosemite but I would be surprised if that was the cause.
What version of Mac are you using, is it a model which supports USB Booting?
Assuming Windows is installed correctly on the SSD, the other cause may be the Samsung T1’s unique requirement for special drivers in OS X. Have you installed these? http://www.samsung.com/global/business/semiconductor/minisite/SSD/global/html/portablessdt1/support.html
I hope this helps!