Mais alguns dados. Só pra ficar mais fácil de entender, tirei algumas screenshots do problema.
No NetBeans fica assim:

Já na execução, fica assim:

E esse é o código gerado pelo NetBeans, lembrando que a fonte do jTextArea1 está como “Derive the font from the default font”. Se eu colocar uma fonte direta nesta propriedade, o código jTextArea.setFont() desaparece, mas o resultado é o mesmo:
private void initComponents() {
jPanel1 = new javax.swing.JPanel();
jcobAno = new javax.swing.JComboBox();
jLabel1 = new javax.swing.JLabel();
jcobMes = new javax.swing.JComboBox();
jLabel2 = new javax.swing.JLabel();
jchbSobrescever = new javax.swing.JCheckBox();
jScrollPane1 = new javax.swing.JScrollPane();
jTextArea1 = new javax.swing.JTextArea();
jProgressBar = new javax.swing.JProgressBar();
jbtnCancelar = new javax.swing.JButton();
jbtnImportar = new javax.swing.JButton();
jScrollPane2 = new javax.swing.JScrollPane();
jtxaLog = new javax.swing.JTextArea();
setDefaultCloseOperation(javax.swing.WindowConstants.DISPOSE_ON_CLOSE);
setTitle("Importar bilhetes do Mesa PC");
setFont(new java.awt.Font("Tahoma", 0, 11));
setLocationByPlatform(true);
jPanel1.setBorder(javax.swing.BorderFactory.createTitledBorder("Bilhetes"));
jLabel1.setText("Ano");
jcobMes.setModel(new javax.swing.DefaultComboBoxModel(new String[] { "Janeiro", "Fevereiro", "Março", "Abril", "Maio", "Junho", "Julho", "Agosto", "Setembro", "Outubro", "Novembro", "Dezembro" }));
jcobMes.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jcobMesActionPerformed(evt);
}
});
jLabel2.setText("Mês");
jchbSobrescever.setText("Sobrescrever bilhetes já importados");
jchbSobrescever.setBorder(javax.swing.BorderFactory.createEmptyBorder(0, 0, 0, 0));
jchbSobrescever.setMargin(new java.awt.Insets(0, 0, 0, 0));
jScrollPane1.setBorder(javax.swing.BorderFactory.createEmptyBorder(1, 1, 1, 1));
jTextArea1.setColumns(20);
jTextArea1.setEditable(false);
jTextArea1.setFont(jTextArea1.getFont()); /* <<<< código estranho */
jTextArea1.setLineWrap(true);
jTextArea1.setText("Para que a importação funcione, os bilhetes já devem estar importados pelo Mesa PC e este deve estar fechado. Esta é uma limitação dos arquivos mdb (Access)");
jTextArea1.setWrapStyleWord(true);
jTextArea1.setBorder(javax.swing.BorderFactory.createEmptyBorder(1, 1, 1, 1));
jTextArea1.setOpaque(false);
jScrollPane1.setViewportView(jTextArea1);
javax.swing.GroupLayout jPanel1Layout = new javax.swing.GroupLayout(jPanel1);
jPanel1.setLayout(jPanel1Layout);
jPanel1Layout.setHorizontalGroup(
jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, jPanel1Layout.createSequentialGroup()
.addContainerGap()
.addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addComponent(jScrollPane1, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 437, Short.MAX_VALUE)
.addGroup(jPanel1Layout.createSequentialGroup()
.addComponent(jLabel2)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jcobMes, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addGap(24, 24, 24)
.addComponent(jLabel1)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jcobAno, javax.swing.GroupLayout.PREFERRED_SIZE, 74, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED, 29, Short.MAX_VALUE)
.addComponent(jchbSobrescever)))
.addContainerGap())
);
jPanel1Layout.setVerticalGroup(
jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(jPanel1Layout.createSequentialGroup()
.addGroup(jPanel1Layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jLabel2)
.addComponent(jcobMes, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jLabel1)
.addComponent(jcobAno, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addComponent(jchbSobrescever))
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jScrollPane1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addContainerGap(javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE))
);
jProgressBar.setMaximum(1000);
jbtnCancelar.setText("Cancelar");
jbtnCancelar.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jbtnCancelarActionPerformed(evt);
}
});
jbtnImportar.setText("Importar");
jbtnImportar.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
jbtnImportarActionPerformed(evt);
}
});
jtxaLog.setColumns(20);
jtxaLog.setFont(new java.awt.Font("Tahoma", 0, 10));
jtxaLog.setRows(5);
jScrollPane2.setViewportView(jtxaLog);
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(javax.swing.GroupLayout.Alignment.TRAILING, layout.createSequentialGroup()
.addContainerGap()
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.TRAILING)
.addComponent(jScrollPane2, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 469, Short.MAX_VALUE)
.addComponent(jPanel1, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, Short.MAX_VALUE)
.addGroup(layout.createSequentialGroup()
.addComponent(jbtnImportar)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jbtnCancelar))
.addComponent(jProgressBar, javax.swing.GroupLayout.Alignment.LEADING, javax.swing.GroupLayout.DEFAULT_SIZE, 469, Short.MAX_VALUE))
.addContainerGap())
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addGroup(layout.createSequentialGroup()
.addContainerGap()
.addComponent(jPanel1, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jScrollPane2, javax.swing.GroupLayout.DEFAULT_SIZE, 125, Short.MAX_VALUE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addComponent(jProgressBar, javax.swing.GroupLayout.PREFERRED_SIZE, javax.swing.GroupLayout.DEFAULT_SIZE, javax.swing.GroupLayout.PREFERRED_SIZE)
.addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
.addGroup(layout.createParallelGroup(javax.swing.GroupLayout.Alignment.BASELINE)
.addComponent(jbtnImportar)
.addComponent(jbtnCancelar))
.addContainerGap())
);
pack();
}