Please post session log files showing upload both from GUI and the script (of the same files). And a log showing GUI reading the directory without times after the script upload.

WinSCP version: 6.1 (issue has occurred with previous versions as well)
Windows version: Windows Server 2012 R2 Std.
Protocal: FTP
GUI interface: Commander
No error message

Issue: When the FTP transfer is done within Commander using "Upload", the receiving directory's "Changed" column shows Date AND Time.
If I use "Generate Code", the resulting script performs the transfer, but only the Date shows in the same directory's "Changed" column - no time value.
The outside program monitoring the receiving directory only processes files that have both Date AND Time. Files with Date only remain in the directory, unprocessed.