I have had the same issue with the latest AdRotate release. It appears there is some new/modified CSS code which applies a max-height property. If you are applying your own margin/padding between ads in a block, you need to make sure you cancel out the max-height. e.g.
.block_outer{
max-height: none !important;
}
.block_outer>div{
margin-bottom: 10px;
}
