You can increase the connection timeout in the Preferences under the Connection section or per-site via the Site Manager.
There's no way to prevent FlashFXP from listing the content of a folder, a general rule of thumb is to keep the amount of files in a folder to under 2k, though 1k or less is even better.
On shared hosting plan some providers cram as many customers as they can into a single psychical server and throttle ftp, this can result in longer than normal delays when listing the content of a folder.
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