You changed the naming convention for temp files in ...\Local Settings\Temp. Version 2008.1 is using a directory name starting with scp$ while 3.5 used a name starting with la$
WinSCP stores temporary files in the TEMP folder in directories beginning with scp (no $). So if 2008.1 is running, and WinSCP starts, it tries to clean up old folders starting with scp. Oops, not their folder. But does warn you about it.
Why the change from la$ to scp$? This is an annoyance that will keep me using 3.5 over 2008.1 as I use WinSCP extensively.