If you have issues with the ftp adapter, below listed are a few hot fixes from Microsoft:
The FTP adapter stops processing the file transfer in a Microsoft BizTalk Server 2006 environment after a network connection recovers
The BizTalk FTP Adapter reports that no files are available even though the files exist when you try to connect to a GXS server in BizTalk Server 2006 R2
The BizTalk 2006 FTP adapter does not retrieve a file from an FTP server when you issue the RETR command
If there are any more out there, let me know