OK, I figured it out. This should help someone who runs into the same problem.
After further review, I determined that the import process doesn't know how to handle MIME messages in the "s" field of the bugevent table. It looks like Fogbuz will store the entire email with all its MIME parts. Fogbugz will also store a plain text version in the "sHTML" field in the bugevent table. So you only need to copy the data in "sHTML" into "s" to have the description show up on the imported issues.
I looked into the description field in the JIRA database and it is blank on these types of Fogbugz issues. You can simply click on the description edit to see that there isn't anything. By looking at the data in the database directly, I was able to verify that it wasn't something in JIRA that could not render the data.
You can see if this is the case in your Fogbugz instance by running a select statement against the Fogbugz database. The results should show you all the rows that have MIME data in the "s" field.
select * from bugevent where femail = 1 and s like '%MIME%';
Before you run the update command, you should backup your Fogbugz database and run tests against a development database prior to doing this in production. You should also verify that all issues in the project have the correct data as this could cause problems with your instance. I would even make a copy of your production Fogbugz database and run the below statement and import from database copy, so as to not cause any side effects with Fogbugz. The below SQL statement was used to fix the problem in our instance.
update bugevent set s = shtml where femail = 1 and s like '%MIME%';
Atlassian may want to open a case. I looked and couldn't find any cases with this issue. In the meantime, the above is a good workaround until then.
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