We have a similar system and it is working perfectly.
I suggest verifying the Intel® SSD is connected to the Full-Mini Card connector (labeled B in page 15). It is the slot on top.
Please share a screenshot of the BIOS (Advanced, Devices, SATA) and the BIOS version.
Cold boot and restart doesnt make a difference. The card is installed correctly. Ive since purchased a Crucial 120GB M500 (CT120M500SSD3) Which is listed as being tested and working with the D54250WYK. This SSD worked straight away after installation with no issues. So I guess either, the intel SSD is not supported (unless someone has used this specific model successfully) or the intel SSD i purchased is faulty (again would really like to know if anyone has used this model successfully in this kind of setup). Either way the system works now with the new SSD.