Check whether local time and remote file time are of the same time zone. If not, go to [Advanced Site Settings | Files | Server Time Offset] and enter a proper value. Suppose you see a newly uploaded file in the Remote Browser Pane has a timestamp of 13:30, while the time of your system clock is 21:30, then you should enter a server time offset value of 8 (hours).
Although it doesn't automatically disconnect the next sync task will still be launched timely, and the ftp site in the next sync task will then be connected. To force disconnecting from a site after a scheduled transfer is finished, use [Options | Events | On transfer complete | Disconnect from site].
Enable [Advanced Site Settings | Synchronization | Ignore file name case].
Enable [Advanced Site Settings | Synchronization | Compare file size rather than file time].
You might have another profile of the same address but different port (21) stored in your Address Book in a position ahead of the 990 one. In this case TurboFTP uses the one with matching address that it first finds in Address Book. If so what you should do is either to remove the 21 one or to use a different address for one of them (for example, IP address), with another using domain address.