Cute FTP is set up to transfer files simulteously instead of sequentiallly , this will overload either the server or your computer. (some security software will prevent too many connections from one IP-address)
Some of the variables affecting throughput are the number of files being transferred, the individual file sizes and whether or not you want to open only one session or have multiple simultaneous sessions to the remote host. We recommend the following guidelines:
1. Multi-Part Transfers. If you are transferring one or more large-size files, use the Multi-Part transfer capability. (File > Download Advanced > Download Multi-part) Make certain that multiple connections are allowed for the site under Tools > Global Options > Connection. When transferring large files in this manner, you should see significant increases in speed. For more information about multi-part transfers, please see the CuteFTP Pro help file topic titled Multi-part (accelerated) transfers.
2. Multiple Simultaneous Transfers. CuteFTP Pro can transfer up to 100 items simultaneously. This capability is useful in situations in which you need to transfer many small to medium size files. Earlier versions of CuteFTP (and most other FTP clients) can only transfer files one at a time (sequentially). To transfer files simultaneously, navigate to Tools > Global Options > Connection and set Per site max connections/transfers to an appropriate limit. Note that setting the limit too high may compromise overall system performance. Once configured, simply drag and drop your files or otherwise transfer them normally and let CuteFTP Pro take care of rest. For more information about multiple simultaneous transfers, please see the help file topic titled Connection options.
3. If your needs are more modest, and you are transferring just one or a relatively few small to medium sized files or if multi-part or multiple simultaneous connections is otherwise not desired, navigate to Tools > Global Options > Connection and make sure that Per site max connections/transfers is set to "1". Then navigate to Tools > Global Options > Transfer and select the Transfer files over the browse session check box. Doing so configures CuteFTP Pro so that a new session is not opened for each transfer. Otherwise, opening a new session for each transfer can take a few seconds and can effectively increase the overall transfer time when compared to some older versions of CuteFTP which always transferred files over the same session.