I have some problems with the new phped 3.3.3 build 3389 when I'm uploading some files to an FTP server. I've just upgraded from version 3.2.1 and didn't ever have to specify anything like "Top publishing directory", just set up the FTP account and it worked. Now I get an error "Failed to upload. No publishing file specified for local file W:\index.php. See project properties.". What has changed? And how could I reach the same it was in version 3.2.1? Thanks for any aplicable answers

Probably you had different settings in 3.2.
To have a file uploaded you have to specify where it should be uploaded to. In this order you should specify publishing account, local root difrectory and corresponding publishing root directory.