Thanks so much for your help. I installed the latest build, but unfortunately it's still not working for me. I tried adding the regex in the per-site skip list as well as in the global skiplist, but it still doesn't work. Here are the settings in case I'm doing something wrong:
I also tried closing and re-opening FlashFXP, but .js files are still transferred.
I'm sure you don't have a lot of time to keep working on this, but if you have any other suggestions or ideas that would be great.