I'm having the same issue. On my end, I killed the allied MCV before it loaded into the transport as it glitched out trying to get in. Then I captured the radar tower, then I deployed my second MCV on the center island.
I'm wondering if not letting the allied MCV deploy on the center island was what caused it.
I've killed the MCV if I remember correctly, and did the same as you (capture, then deploy the MCV on the second island)
I think the allied MCV has to deploy on the island to get it work...
I hope they will get a way to validate the mission for those who were able to settle a base on the second island without killing any building on it.
