Same here. Happens semi-randomly. Console reports:

12/10/07 11:46:59 AM Cyberduck[95868] jobjc_mapObjects() collision, objc object 141e30 of type (NSCFTimer) being entered for Java object of class (com/apple/cocoa/foundation/NSTimer) in entry 1cddd090 
12/10/07 11:46:59 AM Cyberduck[95868] existing java object's class is (com/apple/cocoa/foundation/NSTimer) 
12/10/07 11:46:59 AM Cyberduck[95868] no corresponding java entry! (did it get collected?) 
12/10/07 11:46:59 AM [0x0-0x396396].ch.sudo.cyberduck[95868] ObjCJava FATAL: 
12/10/07 11:46:59 AM [0x0-0x396396].ch.sudo.cyberduck[95868] jobjc_mapObjects(): mapping inconsistency -- hashtable entries are not identical 
12/10/07 11:46:59 AM [0x0-0x396396].ch.sudo.cyberduck[95868] ObjCJava Exit 
12/10/07 11:46:59 AM com.apple.launchd[75] ([0x0-0x396396].ch.sudo.cyberduck[95868]) Exited with exit code: 255 

Please let me know if running the latest nightly build from ​http://update.cyberduck.ch/nightly/ does any good.

I just installed the latest nightly (3348) and it's just quitting on me randomly. I can't seem to find any pattern either. Here's my console report.

12/13/07 3:16:05 PM Cyberduck[7010] jobjc_mapObjects() collision, objc object 13fb80 of type (NSCFTimer) being entered for Java object of class (com/apple/cocoa/foundation/NSTimer) in entry 1b2ab240 
12/13/07 3:16:05 PM Cyberduck[7010] existing java object's class is (com/apple/cocoa/foundation/NSTimer) 
12/13/07 3:16:05 PM Cyberduck[7010] no corresponding java entry! (did it get collected?) 
12/13/07 3:16:05 PM [0x0-0x4aa4aa].ch.sudo.cyberduck[7010] ObjCJava FATAL: 
12/13/07 3:16:05 PM [0x0-0x4aa4aa].ch.sudo.cyberduck[7010] jobjc_mapObjects(): mapping inconsistency -- hashtable entries are not identical 
12/13/07 3:16:05 PM [0x0-0x4aa4aa].ch.sudo.cyberduck[7010] ObjCJava Exit 
12/13/07 3:16:05 PM com.apple.launchd[70] ([0x0-0x4aa4aa].ch.sudo.cyberduck[7010]) Exited with exit code: 255 

Yes, still happens with the latest nightly (3353). Same console output:

12/17/07 9:52:53 PM Cyberduck[1579] jobjc_mapObjects() collision, objc object 141bb0 of type (NSCFTimer) being entered for Java object of class (com/apple/cocoa/foundation/NSTimer) in entry 1be6a440 
12/17/07 9:52:53 PM Cyberduck[1579] existing java object's class is (com/apple/cocoa/foundation/NSTimer) 
12/17/07 9:52:53 PM Cyberduck[1579] no corresponding java entry! (did it get collected?) 
12/17/07 9:52:53 PM [0x0-0x5e05e].ch.sudo.cyberduck[1579] ObjCJava FATAL: 
12/17/07 9:52:53 PM [0x0-0x5e05e].ch.sudo.cyberduck[1579] jobjc_mapObjects(): mapping inconsistency -- hashtable entries are not identical 
12/17/07 9:52:53 PM [0x0-0x5e05e].ch.sudo.cyberduck[1579] ObjCJava Exit 
12/17/07 9:52:53 PM com.apple.launchd[94] ([0x0-0x5e05e].ch.sudo.cyberduck[1579]) Exited with exit code: 255

I have the same issue as well using the latest nightly build I installed today and also using leopard. Cyberduck disapeers within minutes if I upload two folders with numerous files simultaneously.

However if i only upload 1 folder at a time, it doesn't disappear. But... after a few minutes of uploading the "transfers" window shows the transfer as being "incomplete" and I need to run the "resume" function to get it to upload again.

Today I was uploading a folder with hundreds of files, and literally needed to run the "resume" feature about 20-30 times. I get no timeout errors, I get no errors at all. The "Transfer" of the folder just changes from "uploading" to "incomplete" with no messages or warnings.

Forgot to mention I also see similar errors in the console that "Greenskin" posted. And I can make cyberduck disappear on command, just by trying to upload more then 1 folder at time to the same ftp server.

Issues like this should be resolved by a refactored access to non-thread safe method calls in the Cocoa Framework. In r3377.