I have some kind of the same problem. I found your post and one from Richard Davis (quoted at the end of this post) describing some sort of the same problem, but neither of your posts have a reply with a solution.
Have you realized, or someone else, what should be done in order to solve this problem with Rank and File? I'm runing Rank & File v. 1.16, on a Mac, with CS5.
What's the current version of Rank and File Lite and how do I get a copy?
I've been seeing some buggy performance with R+F Lite on Bridge CS5. It reports all the files have been updated but only the first 12 ~ 16 files are actually updates so I have to use it in small chunks which is very frustrating. I checked the version I'm using at in the .jsx file it says: Version 1.1 -- 4/16/06 so I'm wondering if I have the latest version.