Yes, I chcked for floaters. I had one before, and didn't have that problem after removal. But now I removed anther one and it will not stay submerged anymore. I can't see any floaters still attached to the Cyclops.
I am having a similar problem. It also will not stay submerged. I started a new game after the machine update and built the Cyclops when I scanned all the fragments. For the first few days it worked perfectly. Only to find out it doesn't work anymor…