After looking through the code and many image uploads later...turns out the issue is with the cfhttp call in the ioFileExists function of /farcry/packages/cdn/ftp.cfc :
<cfhttp url="http:#getURLPath(config=arguments.config,file=arguments.file)#" method="HEAD" />
This returns a 404, so the GenerateImage function doesn't auto-generate the images. However, the source image does get copied into the Thumbnail directory. The only way I've been able to get the auto-generated images created is to make a call before that line of code above executes. I'm using Limelight as the CDN. Maybe Limelight needs the file content to be called first before it'll return header information? I also tried changing the method to "get" in ftp.cfc, but that still returned a 404.
I made a project copy of image.cfc and added the following within the clause that runs after the source image is copied into the thumbnail folder in the "ImageAutoGenerateBeforeSave" function:
<cfif isdefined("stResult.value") and len(stResult.value)>
<cfset thisURL = application.fc.lib.cdn.getLocation('images').urlPathPrefix & stResult.value>
<cfhttp url="http:#thisURL#" method="get">
It seems to be working, though, I wonder if there's a better way to handle this.