When uploading from your computer FlashFXP will scan the queued folders to calculate a total size that is used for the estimated queue remaining time, so you shouldn't have to expand the folders unless they're on a removable drive or network share.
Does the folder structure contain many sub-folders and files?
When you add the folder to the queue for upload; take a look at the entry in the the queue window, does it show an accurate size for the content within the folder?
(like the image below)