Helpdesk Solution does not convert HTML to plain text. Helpdesk Solution only asks the POP3 server for both a raw copy and a plain text copy of the email. If the POP3 does not provide a plain text version of the email, Helpdesk Solution just uses the raw copy of the email.
To make it so that HTML does not show in the tickets from an email, you will need to make changes on your Mail server so that it will accept requests for plain text from Helpdesk inbox.
Below is an example on how to do this is for an Exchange Server 2003. For any other email software you will need to contact their support:
In Exchange 2003 System Administrator, go to Organization > Administrative Groups > Organization Name > Servers > Exchange server name > Protocols > Pop3, right-click on Default POP3 Virtual Server,and choose Properties.
Click on the Message Format tab, and make sure that MIME is selected and Provide message body as plain text is selected.
Note: If Exchange 2007 Service Pack 3 is used, the parameters changed that required for this format. Per Microsoft, if you required the earlier behavior of the Best body format option, modify the POP3 settings to use the HTML and alternative text retrieval option (see link to MS article below).
POP3 properties for the Altiris service accounts have been changed to HtmlAndTextAlternative and Use POP3 Protocol Default is set to false.