Addon doesnt work with filtered query.
To make it work you should create class that extends PagedDataProvider and override size() method like:
@Override
public int size(Query<T, T> query) {
int limit = dataProvider.sizeInBackEnd(query) - getPagingControls().getPageLength() * getPagingControls().getPageNumber();
if (limit > getPagingControls().getPageLength())
limit = getPagingControls().getPageLength();
return limit;
}