FULL PRODUCT VERSION :
java version "1.8.0_25"
Java(TM) SE Runtime Environment (build 1.8.0_25-b18)
Java HotSpot(TM) 64-Bit Server VM (build 25.25-b02, mixed mode)

Same error for:

java version "1.7.0_71"
Java(TM) SE Runtime Environment (build 1.7.0_71-b14)
Java HotSpot(TM) 64-Bit Server VM (build 24.71-b01, mixed mode)


ADDITIONAL OS VERSION INFORMATION :
Microsoft Windows [Version 6.1.7601]

A DESCRIPTION OF THE PROBLEM :
When reading data from a CipherInputStream a BadPaddingException is thrown when the stream is closed before everything is read.

REGRESSION.  Last worked in version 8u20

ADDITIONAL REGRESSION INFORMATION: 
java version "1.8.0_20"
Java(TM) SE Runtime Environment (build 1.8.0_20-b26)
Java HotSpot(TM) 64-Bit Server VM (build 25.20-b23, mixed mode)

Also worked with:

java version "1.7.0_67"
Java(TM) SE Runtime Environment (build 1.7.0_67-b01)
Java HotSpot(TM) 64-Bit Server VM (build 24.65-b04, mixed mode)

STEPS TO FOLLOW TO REPRODUCE THE PROBLEM :
- Decrypt an InputStream via CipherInputStream 
- Do not read all bytes from the stream 
- Close the CipherInputStream 

EXPECTED VERSUS ACTUAL BEHAVIOR :
EXPECTED -
Close without exception
ACTUAL -
javax.crypto.BadPaddingException thrown on close

ERROR MESSAGES/STACK TRACES THAT OCCUR :
Exception in thread "main" java.io.IOException: javax.crypto.BadPaddingException: Given final block not properly padded
	at javax.crypto.CipherInputStream.close(CipherInputStream.java:321)
	at temp.EncryptionTest.readData(EncryptionTest.java:88)
	at temp.EncryptionTest.main(EncryptionTest.java:23)
Caused by: javax.crypto.BadPaddingException: Given final block not properly padded
	at com.sun.crypto.provider.CipherCore.doFinal(CipherCore.java:966)
	at com.sun.crypto.provider.CipherCore.doFinal(CipherCore.java:824)
	at com.sun.crypto.provider.BlowfishCipher.engineDoFinal(BlowfishCipher.java:319)
	at javax.crypto.Cipher.doFinal(Cipher.java:2004)
	at javax.crypto.CipherInputStream.close(CipherInputStream.java:314)
	... 2 more

REPRODUCIBILITY :
This bug can be reproduced always.

---------- BEGIN SOURCE ----------
package temp;

import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.InputStream;
import java.io.OutputStream;
import java.security.GeneralSecurityException;
import java.security.SecureRandom;

import javax.crypto.Cipher;
import javax.crypto.CipherInputStream;
import javax.crypto.CipherOutputStream;
import javax.crypto.KeyGenerator;
import javax.crypto.spec.IvParameterSpec;
import javax.crypto.spec.SecretKeySpec;

public class EncryptionTest
{
    public static void main(String[] args) throws Throwable
    {
        EncryptionTest t = new EncryptionTest();
        byte[] d = t.wirteData();
        t.readData(d);
    }
    
    final static int     COUNT_BYTE_TO_WRITE = 999;
    
    final static int     COUNT_BYTE_TO_READ  = 99;
    
    final static boolean ENABLE_WORKAROUND   = false;
    
    Cipher               cipherOut, cipherIn;
    
    SecretKeySpec        key;
    
    byte[]               iv                  = new byte[8]; // Blowfish has 8 IV bytes
                                                            
    public EncryptionTest() throws GeneralSecurityException
    {
        KeyGenerator keygenerator = KeyGenerator.getInstance("Blowfish");
        keygenerator.init(128);
        key = new SecretKeySpec(keygenerator.generateKey().getEncoded(),
                        "Blowfish");
        
        new SecureRandom().nextBytes(iv);
        
        cipherOut = Cipher.getInstance("Blowfish/CBC/PKCS5Padding");
        cipherIn = Cipher.getInstance("Blowfish/CBC/PKCS5Padding");
        
        cipherOut.init(Cipher.ENCRYPT_MODE, key, new IvParameterSpec(iv));
        cipherIn.init(Cipher.DECRYPT_MODE, key, new IvParameterSpec(iv));
        
    }
    
    public byte[] wirteData() throws Throwable
    {
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        try (OutputStream oute = new CipherOutputStream(baos, cipherOut))
        {
            for (int i = 0; i < COUNT_BYTE_TO_WRITE; i++)
                oute.write(0);
            
            System.out.println("Write OK");
        }
        return baos.toByteArray();
    }
    
    public void readData(byte[] buf) throws Throwable
    {
        try (InputStream in = new ByteArrayInputStream(buf);
             InputStream ine = new CipherInputStream(in, cipherIn))
        {
            for (int i = 0; i < COUNT_BYTE_TO_READ; i++)
            {
                int x = ine.read();
                if (x != 0)
                    throw new RuntimeException("0 !=" + x);
            }
            
            if (ENABLE_WORKAROUND)
            {// WORKAROUND: ignore all other bytes
                while (ine.read() >= 0)
                {
                    while (ine.available() > 0)
                        ine.skip(ine.available());
                }
            }
        }
        
        System.out.println("Read OK");
    }
}

---------- END SOURCE ----------

CUSTOMER SUBMITTED WORKAROUND :
Add the following code before closing:

               while (ine.read() >= 0)
                {
                    while (ine.available() > 0)
                        ine.skip(ine.available());
                }