I did search for similar threads and saw a few reports, but nobody posted log files for you, so hopefully I can provide any logs information to help solve this problem. I did perform the initial test with an earlier version, but I just verified the issue still exists with the latest release.
WinSCP Version: 4.3.5 Build 1463
Problem After Upgrade: I don't think I've ever had deep enough file paths to encounter this before
Windows Version: Windows 7 Ultimate x64
Transfer Protocol: SFTP-3
Interface: GUI - Explorer
Can't create file
System Error. Code: 3.
The system cannot find the path specified
Steps to Recreate:
1) Create file path sufficiently deep
For reference, copying starting at the depth of BBBBB-3_3-BBBBBBBBBBBBBBBBBBB instead of AAA_AAAA_AAAAAAAAAAAAAAAAAAA is successful
2) In WinSCP explorer window, drag folder from remote location to desired location in windows explorer, drop folder
Software of Server: I'm not entirely clear what this would mean, but if I can get some direction/information I'm happy to try and get it
I will be emailing the log
**As the reverse: If I copy the files from deeper paths (which is successful then) and then recreate the file structure in my local copy, I can also not copy the full tree back to the remote server. It gives the same error that is given above (error code 3, can't create file)**