What kind of files? What's the protocol you are using? If it's not SFTP can you please post the transcript from the Log Drawer?

Among the missing files are 3 folders containing three of my websites. There is nothing in the Log Drawer. I assume it's SFTP as that is the default for Cyberduck, as set in Preferences.

I can see these folders on the server, they are definitely there, just can't be seen in Cyberduck. I've closed it down and opened it up again, still the same list of files.

Replying to https://www.google.com/accounts/o8/id?id=aitoawn9ohnvcgwrcidngrltxjfwkb4xzu3tnh8:

Among the missing files are 3 folders containing three of my websites. There is nothing in the Log Drawer. I assume it's SFTP as that is the default for Cyberduck, as set in Preferences.

I can see these folders on the server, they are definitely there, just can't be seen in Cyberduck. I've closed it down and opened it up again, still the same list of files.

Can you find any related output in the system.log (/Applications/Utilities/Console.app)?

found this in the console:

Dec  5 18:37:07 flloyd-kennedys-macbook [0x0-0x69069].ch.sudo.cyberduck[568]: 2010-12-05 18:37:07,317 [pool-1-thread-12] ERROR ch.cyberduck.core.ftp.FTPPath - No compatible file listing method found

Any use?

Replying to https://www.google.com/accounts/o8/id?id=aitoawn9ohnvcgwrcidngrltxjfwkb4xzu3tnh8:

found this in the console:

Dec  5 18:37:07 flloyd-kennedys-macbook [0x0-0x69069].ch.sudo.cyberduck[568]: 2010-12-05 18:37:07,317 [pool-1-thread-12] ERROR ch.cyberduck.core.ftp.FTPPath - No compatible file listing method found

Any use?

That helps. You are connecting using FTP. There really should be a transcript available in the log drawer, though.

It looks like that is all I can use with my server - IX Webhosting. Never had any probs before. It was working fine this morning, before I upgraded Cyberduck.

Still nothing in the log drawer. Weird, eh? Makes it pretty difficult to upload files, if the folders aren't showing up.

Did you make sure that the log drawer is open before you connect? Alternatively you can also press the Refresh button when you opened the log drawer.

just connected with log drawer open, this is what I got:

220 iis93 Microsoft FTP Service (Version 5.0).
FEAT
500 'FEAT': command not understood
USER flloyd20
331 Password required for flloyd20.
PASS ********
230 User flloyd20 logged in.
PWD
257 "/flloyd20" is current directory.
NOOP
200 NOOP command successful.
SYST
215 Windows_NT version 5.0
STAT /flloyd20
213-status of /flloyd20:
drwxrwxrwx   1 owner    group               0 Dec  5  0:45 adele.handmadebyflloyd.com
drwxrwxrwx   1 owner    group               0 Jul 26 22:56 being-in-voice.com
drwxrwxrwx   1 owner    group               0 Dec  5  7:49 blog.thundersmouththeatre.com
drwxrwxrwx   1 owner    group               0 Jan 22  2009 contact
-rwxrwxrwx   1 owner    group            3638 Jan 22  2009 favicon.ico
drwxrwxrwx   1 owner    group               0 Jan 22  2009 files
drwxrwxrwx   1 owner    group               0 Dec  3 22:44 flloyd-in-voice.com
drwxrwxrwx   1 owner    group               0 Aug 14  7:33 handmadebyflloyd.com
drwxrwxrwx   1 owner    group               0 Dec 12  2009 handmadebyyou
drwxrwxrwx   1 owner    group               0 Dec  5  2009 images
-rwxrwxrwx   1 owner    group            6807 Dec 12  2009 index.html
-rwxrwxrwx   1 owner    group             397 Sep 10  2008 index.php
-rwxrwxrwx   1 owner    group           43976 Dec 27  2008 joyousbraceletcloseup.jpg
-rwxrwxrwx   1 owner    group           15407 Sep 10  2008 license.txt
-rwxrwxrwx   1 owner    group           39900 Sep  1  2008 logo  image only.jpg
drwxrwxrwx   1 owner    group               0 Dec  3 22:21 logs
drwxrwxrwx   1 owner    group               0 Apr 21  2009 offtheplanetproductions.flloyd-in-voice.com
drwxrwxrwx   1 owner    group               0 Dec 12  2009 page1
drwxrwxrwx   1 owner    group               0 Dec 12  2009 page3
drwxrwxrwx   1 owner    group               0 Dec 12  2009 page4
drwxrwxrwx   1 owner    group               0 Dec 12  2009 page6
drwxrwxrwx   1 owner    group               0 Dec 12  2009 page7
drwxrwxrwx   1 owner    group               0 Dec 12  2009 page8
drwxrwxrwx   1 owner    group               0 Dec 12  2009 page9
-rwxrwxrwx   1 owner    group            7642 Sep 10  2008 readme.html
drwxrwxrwx   1 owner    group               0 Dec 12  2009 rw_common
-rwxrwxrwx   1 owner    group            3175 Dec  3 23:53 thatfile.php
drwxrwxrwx   1 owner    group               0 Oct 15  6:21 thundersmouththeatre.com
-rwxrwxrwx   1 owner    group            1257 Sep 10  2008 wp-cron.php
213 End of status.

the missing folders are mentioned in this - e.g. thundersmouththeatre.com and blog.thundersmouththeatre.com. But they still don't show up in the Cyberduck file list.

Bug introduced in r7794.

In r7926.

Please try the latest ​snapshot build available.

Screen

This happens to me, too.
I tried to download latest nighty build (Version 3.8.2 (8349)), but the problem is still there.
See attachment.