Special characters an issue in reading email from server?

I have an email application that uses javamail 1.4.1 that grabs emails out of flat files and displays the messages on the screen. Until recently, all email was sent within the business, but now they are able to receive emails from any email provider. We've been seeing issues where parts of messages go missing, even links to attachments that don't get displayed to the screen. All of the correct information is in the flat files, but it doesn't get displayed. Does Javamail do anything to handle special characters or is there anything you think I could try to get these messages to display? It's really causing some problems!

As far as I can tell, it's not throwing any exceptions, the only ones I catch in retrieving emails are MessagingException, IOException, and IndexOutOfBoundsException, and I'm not seeing any errors in my log files. The headers are the only thing that come through correctly every time, it's always either the message or attachments that go missing. One of the messages is from a mobile phone, which could be a problem, but we've seen it from our company email addresses too. I'll see if I can get a hold of a sample message to post. In the meantime, what kinds of properties can be set? Is there a good place to look for that?
EDIT: here is a sample message (names have been changed to protect the innocent, also removed attachment encoding)
Return-Path: <[email protected]>
X-Original-To: [email protected]
Delivered-To: [email protected]
Received: from localhost (unknown [IP])
     by company.com (Postfix) with ESMTP id AA0FB52B4F0
     for <[email protected]>; Wed, 17 Dec 2008 12:27:00 +0000 (UTC)
Received: from company.com ([IP])
by localhost (HOST [IP]) (amavisd-new, port 10024)
with ESMTP id 02398-05 for <[email protected]>;
Wed, 17 Dec 2008 06:27:00 -0600 (CST)
Received: from fortimail (unknown [IPADDRESS])
     by company.com (Postfix) with ESMTP id 7EBC7178D95
     for <[email protected]>; Wed, 17 Dec 2008 06:27:00 -0600 (CST)
Received: from atlmtaow03.cingularme.com (atlmtaow03.cingularme.com [IPADDRESS])
     by fortimail with ESMTP id mBHCQvRG003014
     for <[email protected]>; Wed, 17 Dec 2008 06:26:58 -0600
X-Mms-MMS-Version: 18
Date: Wed, 17 Dec 2008 06:31:21 -0600
X-Nokia-Ag-Internal: ; smiltype=true; internaldate=1229517081559
Content-Type: multipart/mixed; boundary="----=_Part_11936491_5421953.1229517081567"
X-Mms-Delivery-Report: 1
Received: from schagw02 ([IPADDRESS]) by atlmtaow03.cingularme.com (InterMail vM.6.01.04.00 201-2131-118-20041027) with ESMTP id <20081217122656.MANG3081.atlmtaow03.cingularme.com@schagw02> for <[email protected]>; Wed, 17 Dec 2008 07:26:56 -0500
X-Mms-Transaction-ID: MMS0000084841772
From: <[email protected]>
To: [email protected]
X-Mms-Message-Class: 0
X-Mms-Read-Reply: 1
Mime-Version: 1.0
Message-ID: <3200553.1229517081568.JavaMail.wluser@schagw02>
X-Mms-Priority: 1
X-Mms-Message-Type: 0
Subject: Multimedia message
X-Nokia-Ag-Version: 2.0
X-Virus-Scanned: amavisd-new at location.company.com
------=_Part_11936491_5421953.1229517081567
Content-Type: text/plain; charset=utf-8
Content-Transfer-Encoding: base64
Content-ID: <slide1.txt>
Content-Location: slide1.txt
Content-Disposition: inline
TG9vawo=
------=_Part_11936491_5421953.1229517081567
Content-Type: image/jpeg
Content-Transfer-Encoding: base64
Content-ID: <1215082150-01.jpg>
Content-Location: 1215082150-01.jpg
Content-Disposition: inline
[Attachment encoding goes here]
------=_Part_11936491_5421953.1229517081567--
Edited by: jlapoint on Dec 22, 2008 9:22 AM

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Our JavaMail-based application reads up to 60,000 emails a day. We recently upgraded to JavaMail 1.4.2 to get more leniency reading poorly formatted messages. So far, it's looking great. We only experienced one issue. Upon upgrading, we stopped being able to receive multiparts sent via Faxcom product. To resolve this, we set the property:
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create or replace
FUNCTION pop3 (
   username   VARCHAR2,
   PASSWORD   VARCHAR2,
   msgnum     NUMBER
   RETURN tstrings PIPELINED
IS
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      RETURN VARCHAR2
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21     pop3:sbssld1 port:110
75     "+OK Lotus Notes POP3 server version Release 8.0.1 ready on SBSSLD1/SBPSS.
47     USER [email protected]
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13     PASS password
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6     RETR 1
17     "+OK 1546 octets
38     *** START OF INTERNET MESSAGE BODY ***
9     Subject:
48     X-KeepSent: A231D6D0:8485FE4B-65257AB1:0022E60F;
23      type=4; name=$KeepSent
46     To: [email protected]
53     X-Mailer: Lotus Notes Release 8.0.1 February 07, 2008
95     Message-ID: <[email protected]mbnpparibasfs.in>
48     From: [email protected]
36     Date: Fri, 9 Nov 2012 11:51:14 +0530
90     X-MIMETrack: Serialize by POP3 Server on SBSSLD1/SBPSS(Release 8.0.1|February 07, 2008) at
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17     MIME-Version: 1.0
37     Content-type: multipart/alternative;
68     "     Boundary="0__=EABBF022DFB16ED68f9e8a93df938690918cEABBF022DFB16ED6""
27     Content-Disposition: inline
(null)     (null)
58     --0__=EABBF022DFB16ED68f9e8a93df938690918cEABBF022DFB16ED6
39     Content-type: text/plain; charset=UTF-8
33     Content-transfer-encoding: base64
(null)     (null)
(null)     (null)
76     DQoNCg0KUmVnYXJkcywNClNoYW5tdWdhbSBOYXRhcmFqYW4uDQpNb2IgOiA5NjI5MjUyNDI1DQpP
76     ZmYgOiAwNDQgMjI1MDQ3MDAgRXh0biA0Nzc5DQoNCiB+SWYgdGhlIGZhY3RzIGRvbuKAmXQgZml0
68     IHRoZSB0aGVvcnksIGNoYW5nZSB0aGUgZmFjdHMu4oCdIC0gQWxiZXJ0IEVpbnN0ZWlu
(null)     (null)
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38     Content-type: text/html; charset=UTF-8
27     Content-Disposition: inline
33     Content-transfer-encoding: base64
(null)     (null)
76     PGh0bWw+PGJvZHk+DQo8cD5SZWdhcmRzLDxicj4NClNoYW5tdWdhbSBOYXRhcmFqYW4uPGJyPg0K
76     TW9iIDogOTYyOTI1MjQyNTxicj4NCk9mZiA6IDA0NCAyMjUwNDcwMCBFeHRuIDQ3Nzk8YnI+DQo8
76     YnI+DQogfklmIHRoZSBmYWN0cyBkb27igJl0IGZpdCB0aGUgdGhlb3J5LCBjaGFuZ2UgdGhlIGZh
60     Y3RzLuKAnSAtIEFsYmVydCBFaW5zdGVpbjxicj4NCjwvYm9keT48L2h0bWw+
(null)     (null)
60     --0__=EABBF022DFB16ED68f9e8a93df938690918cEABBF022DFB16ED6--
(null)     (null)
36     *** END OF INTERNET MESSAGE BODY ***
4     QUIT
42     "+OK Lotus Notes POP3 server signing off.
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So that i can display the saved data in the above table as a mail in my separate application.
Thanks in advance.
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Special characters an issue in reading email from server?

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