I have never used Javamail, but I think the problem may be in the following code:
multipart.addBodyPart(messageBodyPart);
multipart.addBodyPart(attachPart3);
multipart.addBodyPart(attachPart3);
multipart.addBodyPart(messageBodyPart2);
attachPart1.attachFile(attachFile1);
multipart.addBodyPart(attachPart1);
multipart.addBodyPart(messageBodyPart3);
attachPart2.attachFile(attachFile2);
multipart.addBodyPart(attachPart2);
I suggest you review the above to check that it is actually doing what you think it is (or should).