#include <QApplication>
#include <QtGui>
#include <QGraphicsScene>
#include <QGraphicsView>
#include <QGraphicsRectItem>
#include <QGraphicsEffect>
#include <QPainter>
#include <QBitmap>
#include <QDebug>

class MYEffect : public QGraphicsEffect
{
public:
    MYEffect() : QGraphicsEffect() {}
    QRectF boundingRectFor(const QRectF& sourceRect) const{
        return sourceRect;
    }

protected:
    void draw(QPainter* painter){
        QPoint offset;
        Qt::CoordinateSystem system = sourceIsPixmap() ? Qt::LogicalCoordinates : Qt::DeviceCoordinates;
        QPixmap pixmap = sourcePixmap(system, &offset, QGraphicsEffect::NoPad);

        if (pixmap.isNull())
            return;

        qDebug() << pixmap.size();

        painter->save();
        QPainter pixmapPainter(&pixmap);
        pixmapPainter.setRenderHints(painter->renderHints());
        pixmapPainter.setCompositionMode(QPainter::CompositionMode_DestinationIn);
        QTransform worldTransform = painter->worldTransform();
        worldTransform *= QTransform::fromTranslate(-offset.x(), -offset.y());
        pixmapPainter.setWorldTransform(worldTransform);
        //pixmapPainter.fillRect(sourceBoundingRect(), Qt::blue);
        painter->setWorldTransform(QTransform());
        painter->setOpacity(0.5);
        painter->drawPixmap(offset, pixmap);
        painter->restore();
    }
};

int main(int argc, char *argv[])
{
    QApplication app(argc, argv);

    QGraphicsScene scene;
    scene.setSceneRect(0,0,50000,50000);

    MYEffect effect;

    QGraphicsRectItem rItem;
    rItem.setRect(20000,20000,10000,10000);
    rItem.setBrush(Qt::red);
    rItem.setGraphicsEffect(&effect);

    scene.addItem(&rItem);

    QGraphicsView view(&scene);
    view.show();

    view.scale(2,2);

    return app.exec();
}

The behaviour is the same with the build in QGraphicsOpcityEffect

Can you share your code ?