OK - Having read through some of the other threads I did as was suggested earlier and added...
synchronize local -mirror -delete -nopermissions I:\Downloads\synctest\ /mnt/sdg1/files/synctest/
... to my code. Listing the command prompt output below:
batch abort
confirm off
reconnecttime 30
Searching for host...
Connecting to host...
Authenticating...
Using username "bbgmp".
Authenticating with pre-entered password.
Authenticated.
Starting the session...
Reading remote directory...
Session started.
Active session: [1] synctest
12 Apr 2012 09:52 PM <DIR> ..
drwxr-xr-x 3 bbgmp bbgmp 32 Apr 12 22:16:45 2012 .
drwxrwx--- 5 bbgmp bbgmp 45 Apr 12 18:54:07 2012 ..
drwxr-xr-x 2 bbgmp bbgmp 31 Apr 12 22:16:57 2012 sync test directory
Comparing...
Local 'I:\Downloads\synctest' <= Remote '<remote_directory>'
Synchronizing...
Session 'synctest' closed.
> 2012-04-12 22:31:51.179 Script: synchronize local -mirror -delete -nopermissions I:\Downloads\synctest\ /mnt/sdg1/files/synctest/
< 2012-04-12 22:31:51.179 Script: Comparing...
. 2012-04-12 22:31:51.179 Collecting synchronization list for local directory 'I:\Downloads\synctest\' and remote directory '/mnt/sdg1/files/synctest/', mode = 1, params = 5639
. 2012-04-12 22:31:51.179 Listing directory "/mnt/sdg1/files/synctest".
> 2012-04-12 22:31:51.179 Type: SSH_FXP_OPENDIR, Size: 39, Number: 1547
< 2012-04-12 22:31:51.194 Type: SSH_FXP_STATUS, Size: 24, Number: 1284
. 2012-04-12 22:31:51.194 Discarding reserved response
< 2012-04-12 22:31:51.210 Type: SSH_FXP_HANDLE, Size: 13, Number: 1547
> 2012-04-12 22:31:51.210 Type: SSH_FXP_READDIR, Size: 13, Number: 1804
< 2012-04-12 22:31:51.225 Type: SSH_FXP_NAME, Size: 341, Number: 1804
> 2012-04-12 22:31:51.225 Type: SSH_FXP_READDIR, Size: 13, Number: 2060
< 2012-04-12 22:31:51.241 Type: SSH_FXP_STATUS, Size: 28, Number: 2060
< 2012-04-12 22:31:51.241 Status code: 1
> 2012-04-12 22:31:51.241 Type: SSH_FXP_CLOSE, Size: 13, Number: 2308
< 2012-04-12 22:31:51.241 Script: Synchronizing...
. 2012-04-12 22:31:51.241 Synchronizing local directory 'I:\Downloads\synctest\' with remote directory '/mnt/sdg1/files/synctest/', params = 5639
If I compare this to the log output for a manual sync using the GUI, it's very different:
. 2012-04-12 22:36:43.061 Collecting synchronization list for local directory 'I:\Downloads\synctest' and remote directory '/mnt/sdg1/files/synctest', mode = 1, params = 5699
. 2012-04-12 22:36:43.076 Listing directory "/mnt/sdg1/files/synctest".
> 2012-04-12 22:36:43.076 Type: SSH_FXP_OPENDIR, Size: 39, Number: 1547
< 2012-04-12 22:36:43.076 Type: SSH_FXP_STATUS, Size: 24, Number: 1284
. 2012-04-12 22:36:43.076 Discarding reserved response
< 2012-04-12 22:36:43.092 Type: SSH_FXP_HANDLE, Size: 13, Number: 1547
> 2012-04-12 22:36:43.108 Type: SSH_FXP_READDIR, Size: 13, Number: 1804
< 2012-04-12 22:36:43.123 Type: SSH_FXP_NAME, Size: 341, Number: 1804
> 2012-04-12 22:36:43.123 Type: SSH_FXP_READDIR, Size: 13, Number: 2060
< 2012-04-12 22:36:43.139 Type: SSH_FXP_STATUS, Size: 28, Number: 2060
< 2012-04-12 22:36:43.139 Status code: 1
> 2012-04-12 22:36:43.139 Type: SSH_FXP_CLOSE, Size: 13, Number: 2308
. 2012-04-12 22:36:45.510 Synchronizing local directory 'I:\Downloads\synctest\' with remote directory '/mnt/sdg1/files/synctest/', params = 5699
. 2012-04-12 22:36:45.541 Getting size of directory "/mnt/sdg1/files/synctest/sync test directory"
. 2012-04-12 22:36:45.541 Listing directory "/mnt/sdg1/files/synctest/sync test directory".
> 2012-04-12 22:36:45.541 Type: SSH_FXP_OPENDIR, Size: 59, Number: 2571
< 2012-04-12 22:36:45.541 Type: SSH_FXP_STATUS, Size: 24, Number: 2308
. 2012-04-12 22:36:45.541 Discarding reserved response
< 2012-04-12 22:36:45.572 Type: SSH_FXP_HANDLE, Size: 13, Number: 2571
> 2012-04-12 22:36:45.572 Type: SSH_FXP_READDIR, Size: 13, Number: 2828
< 2012-04-12 22:36:45.588 Type: SSH_FXP_NAME, Size: 339, Number: 2828
> 2012-04-12 22:36:45.588 Type: SSH_FXP_READDIR, Size: 13, Number: 3084
< 2012-04-12 22:36:45.604 Type: SSH_FXP_STATUS, Size: 28, Number: 3084
< 2012-04-12 22:36:45.604 Status code: 1
> 2012-04-12 22:36:45.604 Type: SSH_FXP_CLOSE, Size: 13, Number: 3332
. 2012-04-12 22:36:45.650 File: "/mnt/sdg1/files/synctest/sync test directory"
. 2012-04-12 22:36:45.650 Listing directory "/mnt/sdg1/files/synctest/sync test directory".
> 2012-04-12 22:36:45.650 Type: SSH_FXP_OPENDIR, Size: 59, Number: 3595
< 2012-04-12 22:36:45.650 Type: SSH_FXP_STATUS, Size: 24, Number: 3332
. 2012-04-12 22:36:45.650 Discarding reserved response
< 2012-04-12 22:36:45.666 Type: SSH_FXP_HANDLE, Size: 13, Number: 3595
> 2012-04-12 22:36:45.666 Type: SSH_FXP_READDIR, Size: 13, Number: 3852
< 2012-04-12 22:36:45.697 Type: SSH_FXP_NAME, Size: 339, Number: 3852
> 2012-04-12 22:36:45.697 Type: SSH_FXP_READDIR, Size: 13, Number: 4108
< 2012-04-12 22:36:45.713 Type: SSH_FXP_STATUS, Size: 28, Number: 4108
< 2012-04-12 22:36:45.713 Status code: 1
> 2012-04-12 22:36:45.713 Type: SSH_FXP_CLOSE, Size: 13, Number: 4356
. 2012-04-12 22:36:45.713 File: "/mnt/sdg1/files/synctest/sync test directory/sync test file.jpg"
. 2012-04-12 22:36:45.713 Copying "/mnt/sdg1/files/synctest/sync test directory/sync test file.jpg" to local directory started.
. 2012-04-12 22:36:45.713 Binary transfer mode selected.
. 2012-04-12 22:36:45.713 Opening remote file.
> 2012-04-12 22:36:45.713 Type: SSH_FXP_OPEN, Size: 86, Number: 4611
< 2012-04-12 22:36:45.728 Type: SSH_FXP_STATUS, Size: 24, Number: 4356
. 2012-04-12 22:36:45.728 Discarding reserved response
< 2012-04-12 22:36:45.744 Type: SSH_FXP_HANDLE, Size: 13, Number: 4611
> 2012-04-12 22:36:45.744 Type: SSH_FXP_FSTAT, Size: 13, Number: 4872
> 2012-04-12 22:36:45.744 Type: SSH_FXP_READ, Size: 25, Number: 5125
. 2012-04-12 22:36:45.760 3 skipped SSH_FXP_WRITE, SSH_FXP_READ, SSH_FXP_DATA and SSH_FXP_STATUS packets.
< 2012-04-12 22:36:45.760 Type: SSH_FXP_ATTRS, Size: 37, Number: 4872
. 2012-04-12 22:36:45.760 Storing reserved response
< 2012-04-12 22:36:45.994 Status code: 1
. 2012-04-12 22:36:45.994 17 skipped SSH_FXP_WRITE, SSH_FXP_READ, SSH_FXP_DATA and SSH_FXP_STATUS packets.
> 2012-04-12 22:36:45.994 Type: SSH_FXP_CLOSE, Size: 13, Number: 8196
< 2012-04-12 22:36:45.994 Type: SSH_FXP_STATUS, Size: 28, Number: 7429
< 2012-04-12 22:36:45.994 Type: SSH_FXP_STATUS, Size: 28, Number: 7685
< 2012-04-12 22:36:46.009 Type: SSH_FXP_STATUS, Size: 28, Number: 7941
Again, any help would be greatly appreciated. I'm currently out of ideas.