Jarvis - Unfortunatly there's really not a good way to exclude forums from the new posts query. The post table does not contain a column for the forumid that the post is in (only a threadid), so there's really not a way to only exclude certain forums using that query. It *may* be possible if the thread table was joined, but I'm really not sure. I'll take a look a little later and if I come up with something I'll let you know.
eclectica - I tried taking a look at your site to test the problem you're describing, but I didn't see any current posts from forum 5 on your homepage. I would almost bet money though that something else in the news query had to be changed... Specifically, the statement in there that says "WHERE isnews = 'Y'". If that is there, or if it's not there and you're unsure of how to add it back, please post the entire news query here so I can have a look at it. Unless I'm missing something though, there's no way it should be able to display a reply to a thread since only the first post in a thread will have a 'Y' in the isnews column.
Neogen - Was it working before? Have you tried downloading the file from here and uploading the clean/unhacked version? Have you upgraded your vBulletin to a new version lately and perhaps forgotten to make the change to newthread.php?