index.cfm in wwwroot used for all IIS sites

Well, the problem has been solved, but I'm still not entirely satisfied. I actually stumbled further into the problem by discovering that any CF file that existed in my wwwroot folder AND my separate site setup led the file in the wwwroot to be loaded for the separate site; in other words, it wasn't only index.cfm that was loading from the wwwroot, it was any file that existed in both locations. Knowing that, and also that other files that existed in my separate site but NOT in the wwwroot functioned normally, I went ahead and moved the app from our wwwroot to a subdirectory and restarted CF. Now the CF sites setup on separate IPs function as expected.

I'm still not satisfied because I'd think that if having CF files in the wwwroot was problematic, it'd have been immediately evident to people like "duh this is your problem!" So I suspect that somehow the problem actually goes deeper and is probably related to something regarding installation/setup of either CF, IIS or the interaction between the two; your guess is probably better than mine, though!

Go into the CF admin click on the Caching "tab" and make sure the option "Cache web server paths" is unchecked. You cannot cache web server paths on multi-homed servers. Make sure you restart ColdFusion after changing this setting.

Also, instead of eating up 1 IP address per site, consider using host headers. The only time you need a dedicated IP address per site is if you've got an SSL certificate associated with said site.

The home directories are already set for each site setup we have in IIS, and they're all unique. The problem is that we have 2 CF sites setup, one which has been setup for over a year and a half and existed as the only site setup in IIS, and the pages reside in the wwwroot folder; I recently added a second IP and site, and no matter what this site's home directory is set to, it tries to load the index.cfm located in the wwwroot folder rather than the index.cfm located in the site's own home directory.

The curious part is that though the site uses the wrong index.cfm file, it still looks for the images in the correct directory (so that when the page is displayed, the images are broken, as they should be).

Open IIS and select the site you want to manage. In the properties section there should be a setting for the site directory or home folder or something like that (I normally use apache, it's been a while since I've used IIS). Set that to root folder of your website. Then do the same for the other site.