Mail clients like Thunderbird will break long attachment names up into multiple short lines, as per RFC 2231:

Content-Type: application/pdf;
name*0="alreallyreallyreallylongfilenamewithlogsoftextthatshouldlinewrap";
name*1=".pdf"
Content-Transfer-Encoding: base64
Content-Disposition: inline;
filename*0="alreallyreallyreallylongfilenamewithlogsoftextthatshouldline";
filename*1="wrap.pdf"

Unfortunately JavaMail (as of 1.4) does not support this aspect of RFC 2231. JIRA will fail to add the attachment, and in the logs prints something like:

2007-04-11 17:48:28,604 JiraQuartzScheduler_Worker-3 DEBUG [service.util.handler.AbstractMessageHandler] part=javax.mail.internet.MimeBodyPart@13cd5b5
2007-04-11 17:48:28,605 JiraQuartzScheduler_Worker-3 DEBUG [service.util.handler.AbstractMessageHandler] Filename=null, content type=application/pdf;^M
name*0="alreallyreallyreallylongfilenamewithlogsoftextthatshouldlinewrap";^M
name*1=".pdf", content=com.sun.mail.util.BASE64DecoderStream@f27b6e
2007-04-11 17:48:28,605 JiraQuartzScheduler_Worker-3 WARN [jira.issue.managers.DefaultAttachmentManager] Cannot create attachment without a filename - inline content? See http://jira.atlassian.com/browse/JRA-10825 (file=tempattach34617dat).
2007-04-11 17:48:28,605 JiraQuartzScheduler_Worker-3 DEBUG [service.util.handler.AbstractMessageHandler] Encountered an error creating the attachment null for issue TP-39
2007-04-11 17:48:28,605 JiraQuartzScheduler_Worker-3 DEBUG [service.services.mail.MailFetcherService] Deleting Message: <461C92BC.1030609@atlassian.com>

JavaMail may also to even parse the email, and can die with:

2007-04-11 17:50:28,128 JiraQuartzScheduler_Worker-1 ERROR [service.util.handler.CreateIssueHandler] Could not create issue!
javax.mail.internet.ParseException: Missing charset in encoded value: %61%6C%6C%79%6C%6F%6E%67%66%69%6C%65%6E%61%6D%65%77%69%74%68
    at javax.mail.internet.ParameterList.decodeValue(ParameterList.java:385)
    at javax.mail.internet.ParameterList.<init>(ParameterList.java:175)
    at javax.mail.internet.ContentDisposition.<init>(ContentDisposition.java:87)
    at javax.mail.internet.MimeBodyPart.getDisposition(MimeBodyPart.java:1039)
    at javax.mail.internet.MimeBodyPart.getDisposition(MimeBodyPart.java:299)
    at com.atlassian.jira.service.util.handler.AbstractMessageHandler.saveAttachment(AbstractMessageHandler.java:311)
    at com.atlassian.jira.service.util.handler.AbstractMessageHandler.handleMultipart(AbstractMessageHandler.java:295)
    at com.atlassian.jira.service.util.handler.AbstractMessageHandler.createAttachmentsForMessage(AbstractMessageHandler.java:243)
    at com.atlassian.jira.service.util.handler.CreateIssueHandler.handleMessage(CreateIssueHandler.java:202)
    at com.atlassian.jira.service.util.handler.CreateOrCommentHandler.handleMessage(CreateOrCommentHandler.java:115)
    at com.atlassian.jira.service.services.mail.MailFetcherService.run(MailFetcherService.java:190)
    at com.atlassian.jira.service.JiraServiceContainerImpl.run(JiraServiceContainerImpl.java:67)
    at com.atlassian.jira.service.ServiceRunner.execute(ServiceRunner.java:48)
    at org.quartz.core.JobRunShell.run(JobRunShell.java:191)
    at org.quartz.simpl.SimpleThreadPool$WorkerThread.run(SimpleThreadPool.java:516)

In this case, the mail is left in the queue, and you will see these stacktraces repeated in the logs every time the mail service triggers (usu. once a minute).