Yeah, same problem here. Try to do a batch transfer of files in background mode. After I come back, it's only transferred around 15 minutes or so of data, and the "Host is not communicating for more than 15 seconds" prompt comes in. Background process stops at that point and it waits for me to click "Abort". There are two prompts, I'm guessing one for each B/G transfer process.
> 2012-01-10 17:21:06.273 [Background 1] Type: SSH_FXP_LSTAT, Size: 94, Number: 3642887
< 2012-01-10 17:21:06.459 [Background 1] Type: SSH_FXP_STATUS, Size: 24, Number: 3642628
. 2012-01-10 17:21:06.459 [Background 1] Discarding reserved response
< 2012-01-10 17:21:06.610 [Background 1] Type: SSH_FXP_STATUS, Size: 29, Number: 3642887
< 2012-01-10 17:21:06.610 [Background 1] Status code: 2
. 2012-01-10 17:21:06.639 [Background 1] Checking existence of partially transfered file.
> 2012-01-10 17:21:06.639 [Background 1] Type: SSH_FXP_LSTAT, Size: 103, Number: 3643399
< 2012-01-10 17:21:06.800 [Background 1] Type: SSH_FXP_ATTRS, Size: 37, Number: 3643399
. 2012-01-10 17:21:06.800 [Background 1] Resuming file transfer.
. 2012-01-10 17:21:06.800 [Background 1] Opening remote file.
> 2012-01-10 17:21:06.800 [Background 1] Type: SSH_FXP_OPEN, Size: 111, Number: 3643651
< 2012-01-10 17:21:07.022 [Background 1] Type: SSH_FXP_HANDLE, Size: 13, Number: 3643651
> 2012-01-10 17:21:07.037 [Background 1] Type: SSH_FXP_WRITE, Size: 4121, Number: 3644166
. 2012-01-10 17:22:54.037 Initiating key re-exchange (timeout)
. 2012-01-10 17:22:54.552 Doing Diffie-Hellman group exchange
. 2012-01-10 17:22:55.054 Doing Diffie-Hellman key exchange with hash SHA-1
. 2012-01-10 17:22:55.689 Initialised AES-256 SDCTR client->server encryption
. 2012-01-10 17:22:55.721 Initialised HMAC-SHA1 client->server MAC algorithm
. 2012-01-10 17:22:55.721 Initialised zlib (RFC1950) compression
. 2012-01-10 17:22:55.721 Initialised AES-256 SDCTR server->client encryption
. 2012-01-10 17:22:55.721 Initialised HMAC-SHA1 server->client MAC algorithm
. 2012-01-10 17:22:55.721 Initialised zlib (RFC1950) decompression
. 2012-01-10 17:23:04.566 Cached directory change via "/home/user/data/directory" to "/home/user/data/directory".
. 2012-01-10 17:23:04.581 Getting current directory name.
. 2012-01-10 17:23:04.591 Directory content loaded from cache.
. 2012-01-10 17:23:07.610 Changing directory to "subdir".
. 2012-01-10 17:23:07.625 Getting real path for '/home/user/data/directory/subdir'
> 2012-01-10 17:23:07.625 Type: SSH_FXP_REALPATH, Size: 70, Number: 3707408
< 2012-01-10 17:23:07.626 Type: SSH_FXP_STATUS, Size: 24, Number: 4612
. 2012-01-10 17:23:07.626 Discarding reserved response
< 2012-01-10 17:23:07.850 Type: SSH_FXP_NAME, Size: 143, Number: 3707408
. 2012-01-10 17:23:07.916 Real path is '/home/user/data/directory/subdir'
. 2012-01-10 17:23:07.916 Trying to open directory "/home/user/data/directory/subdir".
> 2012-01-10 17:23:07.916 Type: SSH_FXP_LSTAT, Size: 70, Number: 3707911
< 2012-01-10 17:23:08.123 Type: SSH_FXP_ATTRS, Size: 37, Number: 3707911
. 2012-01-10 17:23:08.174 Getting current directory name.
. 2012-01-10 17:23:08.174 Listing directory "/home/user/data/directory/subdir".
> 2012-01-10 17:23:08.174 Type: SSH_FXP_OPENDIR, Size: 70, Number: 3708427
< 2012-01-10 17:23:08.380 Type: SSH_FXP_HANDLE, Size: 13, Number: 3708427
> 2012-01-10 17:23:08.436 Type: SSH_FXP_READDIR, Size: 13, Number: 3708684
< 2012-01-10 17:23:08.674 Type: SSH_FXP_NAME, Size: 408, Number: 3708684
> 2012-01-10 17:23:08.701 Type: SSH_FXP_READDIR, Size: 13, Number: 3708940
< 2012-01-10 17:23:08.946 Type: SSH_FXP_STATUS, Size: 28, Number: 3708940
< 2012-01-10 17:23:08.979 Status code: 1
> 2012-01-10 17:23:08.979 Type: SSH_FXP_CLOSE, Size: 13, Number: 3709700
. 2012-01-10 17:23:10.947 Cached directory change via ".." to "/home/user/data/directory".
. 2012-01-10 17:23:10.963 Getting current directory name.
. 2012-01-10 17:23:10.966 Directory content loaded from cache.
. 2012-01-10 18:22:55.715 Initiating key re-exchange (timeout)
. 2012-01-10 18:22:56.225 Doing Diffie-Hellman group exchange
. 2012-01-10 18:22:56.727 Doing Diffie-Hellman key exchange with hash SHA-1
. 2012-01-10 18:22:57.360 Initialised AES-256 SDCTR client->server encryption
. 2012-01-10 18:22:57.374 Initialised HMAC-SHA1 client->server MAC algorithm
. 2012-01-10 18:22:57.374 Initialised zlib (RFC1950) compression
. 2012-01-10 18:22:57.374 Initialised AES-256 SDCTR server->client encryption
. 2012-01-10 18:22:57.374 Initialised HMAC-SHA1 server->client MAC algorithm
. 2012-01-10 18:22:57.374 Initialised zlib (RFC1950) decompression
. 2012-01-10 18:33:19.975 [Background 2] Waiting for dispatching send buffer timed out, asking user what to do.
. 2012-01-10 18:33:22.319 [Background 2] Asking user:
. 2012-01-10 18:33:22.319 [Background 2] Host is not communicating for 15 seconds.
. 2012-01-10 18:33:22.319 [Background 2]
. 2012-01-10 18:33:22.319 [Background 2] Wait for another 15 seconds? ()
. 2012-01-10 18:33:22.319 [Background 1] Waiting for dispatching send buffer timed out, asking user what to do.
. 2012-01-10 18:33:22.319 [Background 1] Asking user:
. 2012-01-10 18:33:22.319 [Background 1] Host is not communicating for 15 seconds.
. 2012-01-10 18:33:22.319 [Background 1]
. 2012-01-10 18:33:22.319 [Background 1] Wait for another 15 seconds? ()
. 2012-01-10 19:22:57.467 Initiating key re-exchange (timeout)
. 2012-01-10 19:22:57.977 Doing Diffie-Hellman group exchange
. 2012-01-10 19:22:58.477 Doing Diffie-Hellman key exchange with hash SHA-1
. 2012-01-10 19:22:59.112 Initialised AES-256 SDCTR client->server encryption
. 2012-01-10 19:22:59.126 Initialised HMAC-SHA1 client->server MAC algorithm
. 2012-01-10 19:22:59.126 Initialised zlib (RFC1950) compression
. 2012-01-10 19:22:59.127 Initialised AES-256 SDCTR server->client encryption
. 2012-01-10 19:22:59.127 Initialised HMAC-SHA1 server->client MAC algorithm
. 2012-01-10 19:22:59.127 Initialised zlib (RFC1950) decompression
. 2012-01-10 20:22:59.619 Initiating key re-exchange (timeout)
. 2012-01-10 20:23:00.120 Doing Diffie-Hellman group exchange
. 2012-01-10 20:23:00.633 Doing Diffie-Hellman key exchange with hash SHA-1
. 2012-01-10 20:23:01.268 Initialised AES-256 SDCTR client->server encryption
. 2012-01-10 20:23:01.282 Initialised HMAC-SHA1 client->server MAC algorithm
. 2012-01-10 20:23:01.282 Initialised zlib (RFC1950) compression
. 2012-01-10 20:23:01.282 Initialised AES-256 SDCTR server->client encryption
. 2012-01-10 20:23:01.282 Initialised HMAC-SHA1 server->client MAC algorithm
. 2012-01-10 20:23:01.282 Initialised zlib (RFC1950) decompression
. 2012-01-10 21:23:01.323 Initiating key re-exchange (timeout)
. 2012-01-10 21:23:01.838 Doing Diffie-Hellman group exchange
. 2012-01-10 21:23:02.337 Doing Diffie-Hellman key exchange with hash SHA-1
. 2012-01-10 21:23:02.976 Initialised AES-256 SDCTR client->server encryption
. 2012-01-10 21:23:02.990 Initialised HMAC-SHA1 client->server MAC algorithm
. 2012-01-10 21:23:02.990 Initialised zlib (RFC1950) compression
. 2012-01-10 21:23:02.990 Initialised AES-256 SDCTR server->client encryption
. 2012-01-10 21:23:02.990 Initialised HMAC-SHA1 server->client MAC algorithm
. 2012-01-10 21:23:02.990 Initialised zlib (RFC1950) decompression
. 2012-01-10 22:03:40.750 [Background 2] Attempt to close connection due to fatal exception:
* 2012-01-10 22:03:41.727 [Background 2] Terminated by user.
. 2012-01-10 22:03:41.727 [Background 2] Closing connection.
. 2012-01-10 22:03:41.727 [Background 2] Sending special code: 12
. 2012-01-10 22:03:41.727 [Background 2] Sent EOF message
. 2012-01-10 22:03:42.952 [Background 1] Attempt to close connection due to fatal exception:
* 2012-01-10 22:03:45.267 [Background 1] Terminated by user.
. 2012-01-10 22:03:45.267 [Background 1] Closing connection.
. 2012-01-10 22:03:45.267 [Background 1] Sending special code: 12
. 2012-01-10 22:03:45.267 [Background 1] Sent EOF message
. 2012-01-10 22:03:45.267 [Background 2] Looking up host "host.example.com"
. 2012-01-10 22:03:45.270 [Background 2] Connecting to 99.111.22.254 port 22
. 2012-01-10 22:03:46.439 [Background 2] Server version: SSH-2.0-OpenSSH_5.9p1 Debian-2
After hitting Abort twice here, it just seems to hang. Let me know what else you need for testing and debugging.