Digging into the code I found the directory paths being rerenced in the #application.path# structure. In particular, I noticed #application.path.webroot# and #application.path.defaultFilePath# were wrong. The reason for this was an old directory mapping in my ColdFusion administrator which assigned "/" to the webroot of our main site for these particular servers.

I realised that FarCry tried to find the webroot and built other directory paths based on this location, so having this mapping in the CF Administrator was causing conflicts. Fortunately, I remembered the ability to define application-specific mappings in CF 8, so I added the following to my /farcry/projects/[project_name]/www/farcryConstructor.cfm:

<cfset THIS.mappings["/"] = getDirectoryFromPath(getCurrentTemplatePath()) />

After this change was in place, I reinitialized the application and the paths were now all being set correctly.