Various FTP operations in the 'Remote' view cause aptana to freeze up--no amount of waiting has ever allowed Aptana to eventually start responding after this happens. It's most frequent with operations involving moving a file (both with drag and drop and with CTRL+C / CTRL+V) but also happens when expanding directories at times. This happens very frequently (i.e. once every 10 mins). It has never worked properly on my installation.
In what may be related, I sometimes cannot save a remote SFTP file due to a 'file does not exist' error. my ssh session also frequently times out in the terminal pane.