Mistake was in insertRows() method. The incoming row argument variable (which is selected QModelIndex.row() number) was accidentally re-declared in for loop:

for row in range(rows):

I've renamed the argument row variable to postion and the fixed working code is posted below (the proxyB sorting attribute was commented out. It displays the ViewB items as unsorted. This way it is easier to see a "real" items order:

Edited later:

There was a few more tweaks made to the code. There is a lot happening "behind of scenes": before or after insertRows() and removeRows() do their job.

For example:

When we call these methods the first argument supplied must be a QModelIndex's row number. It is going to be used by the methods as a "starting point" or "starting row number" from where the indexes will be added (inserted) or removed: as many as the second integer argument says.

As we know the proxy model's modelIndexess row and column numbers do not match to the associated with them the sourceModel's modelIndexes. Interesting but there is a translation from proxy's row numbers to sourceModel's ones before the row-number-argument is even received by those two methods. It can be seen from a print out: the buttonClicked() method "sends" row 0 while the insertRows() method prints out that it received other than 0 row number (if it was supplied an modelIndex "taken" from by-Proxy-driven TableView with sorting or filtering enabled and active).

Aside from it there is some "intricate" mechanism happening on how these two methods remove or pop the data from the model's self.items variable. removeRows() method kind of "returns" back to itself to finish a job if the row numbers do not follow in a sequence. The fully working code is posted below:

from PyQt4.QtCore import *
from PyQt4.QtGui import *
import sys

class Model(QAbstractTableModel):
    def __init__(self, parent=None, *args):
        QAbstractTableModel.__init__(self, parent, *args)
        self.items = ['Item_A000','Item_B001','Item_A002','Item_B003','Item_B004']
        self.numbers=[20,10,30,50,40]
        self.added=0
    def rowCount(self, parent=QModelIndex()):
        return len(self.items)      
    def columnCount(self, parent=QModelIndex()):
        return 2

    def data(self, index, role):
        if not index.isValid(): return QVariant()
        elif role != Qt.DisplayRole:
            return QVariant()

        row=index.row()
        column=index.column()

        if column==0:
            if row<len(self.items):
                return QVariant(self.items[row])
        elif column==1:
            if row<len(self.numbers):
                return QVariant( self.numbers[row] )
        else:
            return QVariant()

    def removeRows(self, position, rows=1, index=QModelIndex()):
        print "\n\t\t ...removeRows() Starting position: '%s'"%position, 'with the total rows to be deleted: ', rows
        self.beginRemoveRows(QModelIndex(), position, position + rows - 1)       
        self.items = self.items[:position] + self.items[position + rows:]
        self.endRemoveRows()

        return True

    def insertRows(self, position, rows=1, index=QModelIndex()):
        print "\n\t\t ...insertRows() Starting position: '%s'"%position, 'with the total rows to be inserted: ', rows
        indexSelected=self.index(position, 0)
        itemSelected=indexSelected.data().toPyObject()

        self.beginInsertRows(QModelIndex(), position, position + rows - 1)
        for row in range(rows):
            self.items.insert(position + row,  "%s_%s"% (itemSelected, self.added))
            self.added+=1
        self.endInsertRows()
        return True

class Proxy(QSortFilterProxyModel):
    def __init__(self):
        super(Proxy, self).__init__()

    def filterAcceptsRow(self, rowProc, parentProc):  
        modelIndex=self.sourceModel().index(rowProc, 0, parentProc)
        item=self.sourceModel().data(modelIndex, Qt.DisplayRole).toPyObject()

        if item and 'B' in item:
            return True
        else: return False


class MyWindow(QWidget):
    def __init__(self, *args):
        QWidget.__init__(self, *args)
        vLayout=QVBoxLayout(self)
        self.setLayout(vLayout)

        hLayout=QHBoxLayout()
        vLayout.insertLayout(0, hLayout)

        tableModel=Model(self)               

        proxyB=Proxy()
        proxyB.setSourceModel(tableModel)

        self.ViewA=QTableView(self)
        self.ViewA.setModel(tableModel)
        self.ViewA.clicked.connect(self.viewClicked)

        self.ViewB=QTableView(self) 
        self.ViewB.setModel(proxyB)
        self.ViewB.clicked.connect(self.viewClicked)
        self.ViewB.setSortingEnabled(True)
        self.ViewB.sortByColumn(0, Qt.AscendingOrder)
        self.ViewB.setSelectionBehavior(QTableView.SelectRows)

        hLayout.addWidget(self.ViewA)
        hLayout.addWidget(self.ViewB)

        insertButton=QPushButton('Insert Row Above Selection')
        insertButton.setObjectName('insertButton')
        insertButton.clicked.connect(self.buttonClicked)
        removeButton=QPushButton('Remove Selected Item')
        removeButton.setObjectName('removeButton')
        removeButton.clicked.connect(self.buttonClicked)

        vLayout.addWidget(insertButton)
        vLayout.addWidget(removeButton)

    def getZeroColumnSelectedIndexes(self, tableView=None):
        if not tableView: return
        selectedIndexes=tableView.selectedIndexes()
        if not selectedIndexes: return
        return [index for index in selectedIndexes if not index.column()]

    def viewClicked(self, indexClicked):
        print 'indexClicked() row: %s  column: %s'%(indexClicked.row(), indexClicked.column() )
        proxy=indexClicked.model()

    def buttonClicked(self):
        button=self.sender()
        if not button: return

        tableView=None
        if self.ViewA.hasFocus(): tableView=self.ViewA
        elif self.ViewB.hasFocus(): tableView=self.ViewB
        if not tableView: print 'buttonClicked(): not tableView'; return

        zeroColumnSelectedIndexes=self.getZeroColumnSelectedIndexes(tableView)
        if not zeroColumnSelectedIndexes: print 'not zeroColumnSelectedIndexes'; return

        firstZeroColumnSelectedIndex=zeroColumnSelectedIndexes[0]
        if not firstZeroColumnSelectedIndex or not firstZeroColumnSelectedIndex.isValid():
            print 'buttonClicked(): not firstZeroColumnSelectedIndex.isValid()'; return            

        startingRow=firstZeroColumnSelectedIndex.row()
        print '\n buttonClicked() startingRow =', startingRow

        if button.objectName()=='removeButton':            
            tableView.model().removeRows(startingRow, len(zeroColumnSelectedIndexes), QModelIndex())

        elif button.objectName()=='insertButton':
            tableView.model().insertRows(startingRow, len(zeroColumnSelectedIndexes), QModelIndex())


if __name__ == "__main__":
    app = QApplication(sys.argv)
    w = MyWindow()
    w.show()
    sys.exit(app.exec_())