Unable to locate the header files inside subdirectories while migrating to Qt5

I have been migrating from Qt 4.8.5 to Qt 5.3.0 recently, and these are the related information:

• Windows 7 32 bit
• Qt 3.1.1
• MSVC 2010 compiler (Both my Qt versions are pre-compiled package of MSVC2010 edition)
• debugger from Win7 SDK

Now I've been trapped by a problem that I keep getting compilation errors:

fatal error C1083: Cannot open include file

from those header files inside subdirectories, for example, #include "FooFolder/bar.h". The compiler is unable to locate all this kind of headers and I am totally befuddled since:

1. The Intellisense works well.
2. If I change back to old kit Qt 4.8.5, it compiles fine
3. Both kits use the same MSVC compiler.

Here is my .pro file:

QT += core gui script
QT += printsupport

greaterThan(QT_MAJOR_VERSION, 4): QT += widgets

TARGET = MyApp
TEMPLATE = app

SOURCES += main.cpp\
        mainwindow.cpp \
    qcustomplot.cpp \
    dialogs/filterdialog.cpp \
    databox/databox.cpp \
    databox/datom.cpp \
    #... and more FooFolder/bar.cpp

HEADERS  += mainwindow.h \
    qcustomplot.h \
    dialogs/filterdialog.h \
    databox/databox.h \
    databox/datom.h \
    #... and more FooFolder/bar.h        

RESOURCES += \
    resources.qrc

win32: LIBS += -LC:/ADLINK/UDASK/lib/ -lusb-dask \    
INCLUDEPATH += C:/ADLINK/UDASK/include \
DEPENDPATH += C:/ADLINK/UDASK/include \

include(qext/qextserialport.pri)

and here is one of the .h file that files to include other subdirectoried headers

#ifndef SETWINDOW_H
#define SETWINDOW_H
#include <QObject>
#include "databox/databox.h" // <---fatal error C1083: Cannot open include file 

class SetWindow: public QObject
{
    Q_OBJECT

public:
    SetWindow();

public Q_SLOTS:
    void setPointNum(int n);
    void setStepSize(int s);    
    int getPointNum();
    int getStepSize();
    void requestSignal();

Q_SIGNALS:
    void sendParameters(int p, int s);

private:
    QString DynamicString;
    DataBox *presentData;

    int m_PointNum;
    int m_StepSize;
};

#endif // SETWINDOW_H

and the header file failed to be included:

#ifndef DATABOX_H
#define DATABOX_H
#include <QVector>
#include <QFile>
#include <QMap>
#include <QString>
#include "datom.h"

class Measurement
{
public:
    Measurement();
    void setNumChan(int n);
    void setADRange(QString &s);
    void setSamplingRate(int n);
    void setTimeBase(double d);

    int NumChan;
    QString ADRange;
    int SamplingRate;
    double TimeBase;
};

class DataBox
{    
public:
    DataBox();

    void setCurrentFile(QString path);
    void loadData();
    void cleanAll();    

    QVector<double>* py_0;    
    QVector<double>* py_1;
    QVector<double>* ptimeStamp;
    QVector<double>* pi_M;
    QVector<double>* py_M;
    QVector<double>* py_W;

    QMap<double, double> AI_0;
    QMap<double, double> AI_1;
    QMap<int, double> AI0;
    QMap<int, double> AI1;

    double timeBase;

    Measurement parameters;
    QVector<Datom> *dataPoints;

private:
    QString currentFile;
};

#endif // DATABOX_H