Got it!
after hours of messing around the answer manifested itself about 10 minutes after I sign up to a forum and make a post as is the way of things :P
So... I put a "Pause" at the start and end of the batch file, and then I got this gem
then ran the batch file from scheduler and got
so it seems that these applications are doing their own completely different things with relative paths.
changing my batch file to
has worked
So... I put a "Pause" at the start and end of the batch file, and then I got this gem
Cannot open file "C:\Users\username\Documents\script.txt". The system cannot find the file specified
then ran the batch file from scheduler and got
Cannot open file "C:\WINDOWS\system32\script.txt". The system cannot find the file specified
so it seems that these applications are doing their own completely different things with relative paths.
changing my batch file to
"C:\WinSCP.com" /script="C:\script.txt" /log="C:\log.txt"
has worked