I had the same problem recently.  You should check and verify the following: 1. Your MD3000i is set for "unified" mode (switch in up position, single disk set light displayed on front). 2. Your MD1000 is also in "unified mode" (you indicate that it is) 3. You have (2) EMM control modules installed in the MD1000. 3. You are cabled correctly between the MD3000i and the MD1000. For redundant paths to work, you should have (2) cables, one from the out port on each of your MD3000i controllers (controller 0 and 1) connecting into the corresponding "in" port on each of the (2) EMMs on your MD1000.  Since you reference only a single cable connection from the MD3000i to the MD1000, it sounds as though your issue is simply that you are not cabled correctly.
I just added a md1000 to my existing MD3000i. I powered on everything and the new md1000 is recognized. But now the md3000i is flashing orange, I check any errors on the MD Storage Manager and I get this error: Expansion Enclosure - Loss of Path Redundancy I have the md1000 set up as a single unit (not split into 2 units) there are 5 drives in slots 10-14 and one cable attaching it to the md300i. What exactly is causing this error and how can I fix it?   Thanks, 
MD3000i Expansion Enclosure - Loss of Path Redundancy