The only other thing that I can think of is the "When to skip" setting.
Are you directly selecting the .js files or are they within a folder that you've queued for transfer?
If you are directly selecting the .js files then they wont be skipped when "Automatic File Transfers" is selected.
Automatic File Transfers
An automatic transfer occurs when FlashFXP en-queues nested files or folders within a folder that was manually queued.
Manual File Transfers
A manual transfer occurs when the user interactively queues or transfers an item.
Both
The skip list is applied to automatic and manual transfers.
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