It's probably just the way the light is hitting it, but that almost looks like a handprint in the top left of the first two pictures in that series.

I'd read that cup and ring marks were actually found under the water, with no references, and spent a fruitless hour following links trying to find out more, and lost where I'd first seen it mentioned.

I saw this about Crannogs in the Orkneys on the Orkneyjar page. Their website is usually updated quite frequently, so I guess they are still awaiting help from the underwater archaeology trust to look into these.
http://www.orkneyjar.com/archaeology/voycrannogs.htm