We SAW the Shemona kiss but not the boat kiss, this was I believe a conscious decision by TPTB to make one ambiguous (Leonard) and one (Sheldon) clearly defined.
I have allways considered that given leonards vague description what happend in Sheldons office is also what happened on the boat an uninitiated kiss which was quickly ended.
Neither are cheating. If anything penny went immediately defensive and in my opinion over reacted where as amy waited for the details before judging.
I also believe this was intintional by TPTB to further the view of both guys that they wanted to convey to the audience at the time, Leonard bad, Sheldon good.
Edit: I also think that if Molero had still been in charge the boat kiss WOULD have been brought up in 11.01 to sheldons benefit and leonards detriment