I'm in the process of updating the site's software for both Movable Type and the forum. This may cause issues in the near future. This process started last week, but the problem has expanded a bit, so I'm still working through a few things.
Unfortunately, this site seems to have become the target of some malicious hackers who are exploiting some sort of vulnerability to inject code into some index files. Near as I can tell, the blog is among the least affected sections of the site (perhaps because it is consistently refreshed (and thus overwritten)). At this point, I think I've done everything I can do. I've contacted my host as well, so hopefully they can help me diagnose the problem. Sorry for any inconvenience. Hopefully this will be resolved soon.
Update: Spoke with my host. They inspected my account and all appears to be well for now. The recommended using some different FTP and account settings, but otherwise I seem to have done all that I can at this point. Software updated, passwords changed, all known issues removed, etc... I'll just have to keep an extra close eye on the site for the time being.
Again Update: It appears that the upgrade to Movable Type broke the pagination at the bottom of the page. It wasn't working for a few days, but it appears to be fixed now.