A couple of things I've noticed
It seems that when you get pearls in the red chest from the DC, you don't get the other 30 pearls. I thought it happened about a week ago, but I wasn't 100% positive, and then it happened to me yesterday. I got 40 pearls from the chest, and I noted my total after getting the 40, then when the 30 pearls came up, the graphic was different, in that it didn't show them being added to my total, and sure enough, when I went back to the nest, my total was the same as it was after I got the 40.
The other thing is, it seems you cannot get additional mighty eagle spells anymore. I usually bring all my spells to the hard levels, and yesterday I used ME in the first room, and the destructometer filled up and went to 0 several times without ever replace the spell.
Has anyone else noticed this?