Laxmi-
I wish I could give you better advice, but: increase the perm gen again. I have a stable Fedora 3.5 that runs... well, it just runs. But I give it up to 3G of heap (with no additional permgen setting), and we don't use the Messaging module (so I have no experience there).
More broadly, if there's no issues in Jira or emails to the list about 3.5, you're going to have to take the lead on finding the issues yourself- I would try to upgrade to a more modern version personally, as 3.5 was released quite some time ago and the codebase has changed a great deal since then.
- Ben