Don't panic! Panic just released an update to their uber-popular FTP/SFTP client Transmit which purportedly squashes all those nasty bugs which have been driving you crazy. Version 3.5.4 fixes issues with certain SFTP servers, adds a preference pane to keep you connected even through some troublesome routers, improved WebDAV support and permissions reliability, and fixes an issue with the "Transfer Complete" sound. 3.5.4 also improves overall application stability.
Now, this might seem a bit silly, but my favorite thing about the notification email I received from Panic is the fact that they put a big, prominent download link at the top of the message. Thats the kind of smart thinking and small touches I love and expect from Mac developers.