Okay, I discovered the reason for that problem. It was because of changed window handling between 2005 and 2006 releases, which caused the program to not show any dialogs. This caused the uploads/downloads to be impossible, as well as removing bookmarks, and probably much other stuff. Now I have fixed that as well, and I tried to download files, and it worked.. I couldn't test uploading, because I don't right at the moment have access to ftp server which I have write access to.

The new version is now available for download. I wish the major issues are now fixed.