Well, I can probably explain that. My JAA class 2 medical took something like four hours, including, as I remember, three different eyesight tests, all computerized (sharpness, width of field and color). Plus 3 tubes of blood, urine, general fysiology, hearing, ECG, you name it. In the process I saw at least four different examiners (I don't think they were all qualified doctors, but I would not be surprised).
The FAA class 3 medical only required me to read a few letters from a set distance, just a finger prick of blood and a drop of urine and that was about it. In and out in less than an hour, and that included 30 minutes waiting for the other flight student who was with me.
So I'm not surprised that a JAA class 2 finds more things than an FAA class 3.