Code:
System.err.println("START DEBUG:");
System.setProperty("javax.activation.debug", "true");
Thread.currentThread().setContextClassLoader(this.getClass().getClassLoader());
MailcapCommandMap cMap = (MailcapCommandMap) CommandMap.getDefaultCommandMap();
cMap.addMailcap("text/plain; ; x-java-content-handler=com.sun.mail.handlers.text_plain");
cMap.addMailcap("text/html; ; x-java-content-handler=com.sun.mail.handlers.text_html");
cMap.addMailcap("text/xml; ; x-java-content-handler=com.sun.mail.handlers.text_xml");
cMap.addMailcap("multipart/*; ; x-java-content-handler=com.sun.mail.handlers.multipart_mixed; x-java-fallback-entry=true");
cMap.addMailcap("message/rfc822; ; x-java-content-handler=com.sun.mail.handlers.message_rfc822");
System.err.println("END DEBUG:");

Working System:
12:25:53 AM [SEVERE] START DEBUG:
12:25:53 AM [INFO] MailcapCommandMap: load HOME
12:25:53 AM [INFO] new MailcapFile: file C:\Users\Cody\.mailcap
12:25:53 AM [INFO] MailcapCommandMap: load SYS
12:25:53 AM [INFO] new MailcapFile: file C:\Program Files\Java\jre7\lib\mailcap
12:25:53 AM [INFO] MailcapCommandMap: load JAR
12:25:53 AM [INFO] MailcapCommandMap: getResources
12:25:53 AM [INFO] MailcapCommandMap: URL jar:file:/F:/Minecraft/Test%20Server/lib/mail.jar!/META-INF/mailcap
12:25:53 AM [INFO] new MailcapFile: InputStream
12:25:53 AM [INFO] parse: text/plain;;		x-java-content-handler=com.sun.mail.handlers.text_plain
12:25:53 AM [INFO]   Type: text/plain
12:25:53 AM [INFO]     Command: content-handler, Class: com.sun.mail.handlers.text_plain
12:25:53 AM [INFO] parse: text/html;;		x-java-content-handler=com.sun.mail.handlers.text_html
12:25:53 AM [INFO]   Type: text/html
12:25:53 AM [INFO]     Command: content-handler, Class: com.sun.mail.handlers.text_html
12:25:53 AM [INFO] parse: text/xml;;		x-java-content-handler=com.sun.mail.handlers.text_xml
12:25:53 AM [INFO]   Type: text/xml
12:25:53 AM [INFO]     Command: content-handler, Class: com.sun.mail.handlers.text_xml
12:25:53 AM [INFO] parse: multipart/*;;		x-java-content-handler=com.sun.mail.handlers.multipart_mixed; x-java-fallback-entry=true
12:25:53 AM [INFO]   Type: multipart/*
12:25:53 AM [INFO]     Command: content-handler, Class: com.sun.mail.handlers.multipart_mixed
12:25:53 AM [INFO] parse: message/rfc822;;	x-java-content-handler=com.sun.mail.handlers.message_rfc822
12:25:53 AM [INFO]   Type: message/rfc822
12:25:53 AM [INFO]     Command: content-handler, Class: com.sun.mail.handlers.message_rfc822
12:25:53 AM [INFO] MailcapCommandMap: successfully loaded mailcap file from URL: jar:file:/F:/Minecraft/Test%20Server/lib/mail.jar!/META-INF/mailcap
12:25:53 AM [INFO] MailcapCommandMap: load DEF
12:25:53 AM [INFO] MailcapCommandMap: not loading mailcap file: /META-INF/mailcap.default
12:25:53 AM [INFO] MailcapCommandMap: add to PROG
12:25:53 AM [INFO] new MailcapFile: default
12:25:53 AM [INFO] appendToMailcap: text/plain; ; x-java-content-handler=com.sun.mail.handlers.text_plain
12:25:53 AM [INFO] parse: text/plain; ; x-java-content-handler=com.sun.mail.handlers.text_plain
12:25:53 AM [INFO]   Type: text/plain
12:25:53 AM [INFO]     Command: content-handler, Class: com.sun.mail.handlers.text_plain
12:25:53 AM [INFO] MailcapCommandMap: add to PROG
12:25:53 AM [INFO] appendToMailcap: text/html; ; x-java-content-handler=com.sun.mail.handlers.text_html
12:25:53 AM [INFO] parse: text/html; ; x-java-content-handler=com.sun.mail.handlers.text_html
12:25:53 AM [INFO]   Type: text/html
12:25:53 AM [INFO]     Command: content-handler, Class: com.sun.mail.handlers.text_html
12:25:53 AM [INFO] MailcapCommandMap: add to PROG
12:25:53 AM [INFO] appendToMailcap: text/xml; ; x-java-content-handler=com.sun.mail.handlers.text_xml
12:25:53 AM [INFO] parse: text/xml; ; x-java-content-handler=com.sun.mail.handlers.text_xml
12:25:53 AM [INFO]   Type: text/xml
12:25:53 AM [INFO]     Command: content-handler, Class: com.sun.mail.handlers.text_xml
12:25:53 AM [INFO] MailcapCommandMap: add to PROG
12:25:53 AM [INFO] appendToMailcap: multipart/*; ; x-java-content-handler=com.sun.mail.handlers.multipart_mixed; x-java-fallback-entry=true
12:25:53 AM [INFO] parse: multipart/*; ; x-java-content-handler=com.sun.mail.handlers.multipart_mixed; x-java-fallback-entry=true
12:25:53 AM [INFO]   Type: multipart/*
12:25:53 AM [INFO]     Command: content-handler, Class: com.sun.mail.handlers.multipart_mixed
12:25:53 AM [INFO] MailcapCommandMap: add to PROG
12:25:53 AM [INFO] appendToMailcap: message/rfc822; ; x-java-content-handler=com.sun.mail.handlers.message_rfc822
12:25:53 AM [INFO] parse: message/rfc822; ; x-java-content-handler=com.sun.mail.handlers.message_rfc822
12:25:53 AM [INFO]   Type: message/rfc822
12:25:54 AM [INFO]     Command: content-handler, Class: com.sun.mail.handlers.message_rfc822
12:25:54 AM [SEVERE] END DEBUG:

Non-Working System:
26.10 23:17:50 [Server] SEVERE START DEBUG:
26.10 23:17:50 [Server] SEVERE END DEBUG:



When Casting to Multipart

Working System:
12:32:29 AM [SEVERE] START DEBUG:
12:32:29 AM [INFO] MailcapCommandMap: createDataContentHandler for multipart/mixed
12:32:29 AM [INFO]   search DB #0
12:32:29 AM [INFO]   search DB #1
12:32:29 AM [INFO]   search fallback DB #0
12:32:29 AM [INFO]     got content-handler
12:32:29 AM [INFO]       class com.sun.mail.handlers.multipart_mixed
12:32:29 AM [SEVERE] END DEBUG:

Non-Working System:
26.10 23:13:06 [Server] SEVERE START DEBUG:
26.10 23:13:06 [Server] SEVERE java.lang.ClassCastException: javax.mail.util.SharedByteArrayInputStream cannot be cast to javax.mail.Multipart
26.10 23:13:06 [Server] SEVERE at com.codisimus.plugins.textplayer.TextPlayerMailer.findMimeTypesHelper(TextPlayerMailer.java:423)
26.10 23:13:06 [Server] SEVERE at com.codisimus.plugins.textplayer.TextPlayerMailer.findMimeTypes(TextPlayerMailer.java:400)
26.10 23:13:06 [Server] SEVERE at com.codisimus.plugins.textplayer.TextPlayerMailer.getMsg(TextPlayerMailer.java:384)
26.10 23:13:06 [Server] SEVERE at com.codisimus.plugins.textplayer.TextPlayerMailer.checkMail(TextPlayerMailer.java:225)
26.10 23:13:06 [Server] SEVERE at com.codisimus.plugins.textplayer.TextPlayerMailer$2.run(TextPlayerMailer.java:522)
26.10 23:13:06 [Server] SEVERE at org.bukkit.craftbukkit.scheduler.CraftWorker.run(CraftWorker.java:34)
26.10 23:13:06 [Server] SEVERE at java.lang.Thread.run(Thread.java:722)
26.10 23:13:06 [Server] SEVERE END DEBUG: