Especially check your MySQL logs. The first time that I added fields I neglected to modify the code to ensure that the data would be inserted into the database from email. When a ticket is opened via email it makes some assumptions about things like source, etc. If you required one of your new fields, you will need to provide a "default" value for when a ticket is opened via email. Especially if you have displaying of errors on your webserver shut off.
If I remember correctly you would want to open:
\include\class.mailfetch.php
Look for the createTicket function, and add a line that looks something like
$var = "default value";
This will populate your custom value with something.
